<div dir="ltr"><br><div>Hi Will et al.,</div><div><br></div><div>We have come across an issue when annotating with the --custom option. It seems that the alternative allele is not taken into account for the annotation and therefore the wrong information is associated with the respective allele in almost all cases. I have attached some test data and a test script (test.sh) that runs through all the combinations for sites with 1 and 2 alternative alleles. The annotated transcript of the script can be seen below (correct annotation highlighted in <font color="#6aa84f">green</font>, faulty annotation in <font color="#ff0000">red</font>). A quick fix would be very much appreciated.</div><div><br></div><div>All best,</div><div> Stefan</div><div><br></div><div><br></div><div><div><font face="monospace, monospace">$ . ./test.sh</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>rs35602605<span class="" style="white-space:pre">        </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765,6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC_AC=15765,6;ExAC=rs35602605</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.norm.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.norm=.;ExAC.norm_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.rare.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.rare_AC=6;ExAC.rare=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.common.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.common_AC=15765;ExAC.common=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rev.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>rs35602605<span class="" style="white-space:pre">        </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765,6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC=rs35602605;ExAC_AC=15765,6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rev.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">      </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.norm.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.norm=.;ExAC.norm_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rev.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.rare.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.rare=.;ExAC.rare_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rev.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.common.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A,T<span class="" style="white-space:pre">       </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.common=.;ExAC.common_AC=15765</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_norm.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>rs35602605<span class="" style="white-space:pre">        </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765,6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC_AC=15765,6;ExAC=rs35602605</font></font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">        </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC=rs35602605;ExAC_AC=15765,6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_norm.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.norm.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.norm_AC=6;ExAC.norm=.</font></font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.norm=.;ExAC.norm_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_norm.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.rare.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.rare_AC=6;ExAC.rare=.</font></font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.rare_AC=6;ExAC.rare=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_norm.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.common.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.common=.;ExAC.common_AC=15765</font></font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.common=.;ExAC.common_AC=15765</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_common.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">        </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>rs35602605<span class="" style="white-space:pre">        </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765,6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC=rs35602605;ExAC_AC=15765,6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_common.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.norm.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.norm_AC=6;ExAC.norm=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_common.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">        </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.rare.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.rare=.;ExAC.rare_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_common.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">        </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.common.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.common_AC=15765;ExAC.common=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rare.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>rs35602605<span class="" style="white-space:pre">        </span>G<span class="" style="white-space:pre"> </span>T,A<span class="" style="white-space:pre">       </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765,6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre"> </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC_AC=15765,6;ExAC=rs35602605</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rare.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.norm.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.norm=.;ExAC.norm_AC=6</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rare.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.rare.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">     </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=6</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">       </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#6aa84f">ExAC.rare_AC=6;ExAC.rare=.</font></font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">#INPUT: test_rare.vcf</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">  </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span>.</font></div><div><font face="monospace, monospace">#CUSTOM: ExAC.r0.3.common.vcf.gz</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>2.40354e+07<span class="" style="white-space:pre">       </span>PASS<span class="" style="white-space:pre">      </span>AC=15765</font></div><div><font face="monospace, monospace">=>VEP:</font></div><div><font face="monospace, monospace">15<span class="" style="white-space:pre">   </span>40308859<span class="" style="white-space:pre">  </span>.<span class="" style="white-space:pre"> </span>G<span class="" style="white-space:pre"> </span>A<span class="" style="white-space:pre"> </span>.<span class="" style="white-space:pre"> </span>PASS<span class="" style="white-space:pre">      </span><font color="#ff0000">ExAC.common=.;ExAC.common_AC=15765</font></font></div></div><div><br></div></div>