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Hi Stefan,<br>
<br>
You are correct - custom annotation uses only position information
to extract features. Thanks for pointing out this causes problems
when variants with 2 alternate alleles are split over two lines in
the VCF - we will look at taking allele information into account.<br>
<br>
All the best,<br>
<br>
Sarah <br>
<br>
<div class="moz-cite-prefix">On 01/12/2015 18:26, Stefan Gräf wrote:<br>
</div>
<blockquote
cite="mid:CAFEREoX=YQuN=w85wXKA+iye4wLHUc-tA=R1vOW0t5WZMqcXHw@mail.gmail.com"
type="cite">
<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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
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