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<br>
Hi Stefan,<br>
<br>
This will not be in release 83 when it comes out this week, but will
be available in release 84, if not before.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 04/12/2015 11:31, Stefan Gräf wrote:<br>
</div>
<blockquote
cite="mid:CAFEREoU1P0=6Mv=MD+krCkVJUi-_Hm+LCTe1zAdp7JiquF0ajw@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Sarah,
<div><br>
</div>
<div>Do you have an estimate when this might get resolved?</div>
<div><br>
</div>
<div>Many thanks,</div>
<div> Stefan</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 2 December 2015 at 12:38, Sarah Hunt
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> <br>
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>
<div>
<div class="h5"> <br>
<div>On 01/12/2015 18:26, Stefan Gräf wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>rs35602605<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765,6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.norm.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.rare.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.common.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>rs35602605<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765,6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.norm.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.rare.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.common.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A,T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>rs35602605<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765,6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span><font
color="#ff0000">ExAC_AC=15765,6;ExAC=rs35602605</font></font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.norm.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span><font
color="#ff0000">ExAC.norm_AC=6;ExAC.norm=.</font></font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.rare.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span><font
color="#ff0000">ExAC.rare_AC=6;ExAC.rare=.</font></font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.common.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span><font
color="#6aa84f">ExAC.common=.;ExAC.common_AC=15765</font></font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>rs35602605<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765,6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.norm.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.rare.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.common.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>rs35602605<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T,A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765,6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.norm.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.rare.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=6</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</font></div>
<div><font face="monospace, monospace">#CUSTOM:
ExAC.r0.3.common.vcf.gz</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>2.40354e+07<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>AC=15765</font></div>
<div><font face="monospace, monospace">=>VEP:</font></div>
<div><font face="monospace, monospace">15<span style="white-space:pre-wrap"> </span>40308859<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span>A<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span><font
color="#ff0000">ExAC.common=.;ExAC.common_AC=15765</font></font></div>
</div>
<div><br>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
<span class="">
<pre>_______________________________________________
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</pre>
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