<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi David</p>
<div class="moz-cite-prefix">On 18/06/2019 10:08, David Tamborero
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMk_RaSsX-H5sQoeV3OeUpRHB7PWLesEV1qw0FNfmf__PS2TSg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi Helen,<br>
<div><br>
</div>
<div>(sorry for the late response, i was travelling)</div>
<div><br>
</div>
<div>indeed, it looks like the combo to make the VEP run stop
is:</div>
<div><br>
</div>
<div>- --tab as output format</div>
<div>- the REF==ALT</div>
<div>- the next line to the REF==ALT entry is *a different*
chromosome</div>
<div><br>
</div>
</div>
</blockquote>
There was a bug when the last entry on a chromosome was a variant
with REF==ALT.<br>
We pushed a fix yesterday to our current release (release/96) and it
will be in future releases.<br>
<br>
Thank you for reporting the problem.<br>
<blockquote type="cite"
cite="mid:CAMk_RaSsX-H5sQoeV3OeUpRHB7PWLesEV1qw0FNfmf__PS2TSg@mail.gmail.com">
<div dir="ltr">
<div>on the other hand, regarding the 'concept' of null variant,
do you think that a REF==ALT should be considered as so? I
mean, should not be annotated as silent, as opposite to true
'non valid' variant statements as that passing an ALT of '.' ?</div>
<div><br>
</div>
</div>
</blockquote>
When using the --allow_non_variant VEP expects a non-variant to be
represented with an ALT with the missing value (.)<br>
<br>
If the variant has REF==ALT, the variant is not included in tab
output but included in VCF (with no consequence).
<p>For vcf variants with REF==ALT, vcf-validator warns "REF allele
listed in the ALT field??"</p>
<p>We will review the REF==ALT in VEP and VEP documentation.</p>
<p>Regards<br>
Helen</p>
<p> </p>
<blockquote type="cite"
cite="mid:CAMk_RaSsX-H5sQoeV3OeUpRHB7PWLesEV1qw0FNfmf__PS2TSg@mail.gmail.com">
<div dir="ltr">
<div>thanks!</div>
<div>d</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El jue., 13 jun. 2019 a las
10:06, Helen Schuilenburg (<<a
href="mailto:helens@ebi.ac.uk" target="_blank"
moz-do-not-send="true">helens@ebi.ac.uk</a>>) escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi David<br>
</p>
<div
class="gmail-m_-4451247660575176358gmail-m_-3977281314937812526moz-cite-prefix">On
07/06/2019 18:44, David Tamborero wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Helen
<div><br>
</div>
<div>FYI, if I m not wrong at this time of the day, VEP
run (--tab output) stops<span
style="background-color:rgb(255,255,255)"> </span>(w/o
any msg or warning file created) as soon as a line
with REF==ALT is reached, so it does not seem to need
to 'accumulate' a number of these 'non-variant'
entries </div>
<div>
<div><br>
</div>
</div>
</div>
</blockquote>
I am looking into this. Is the variant following the line
with REF==ALT on the same chromosome?
<blockquote type="cite">
<div dir="ltr">
<div>
<div>on the other hand, as you say, when using vcf as
output with the --allow_non_variant flag, entries as
e.g.</div>
<div><br>
</div>
<div>12 111352091 16500 C C . PASS<br>
</div>
<div><br>
</div>
<div>are included in the output w/o any annotation, </div>
<div><br>
</div>
</div>
</div>
</blockquote>
When using VCF format as input and output, by default VEP
will skip non-variant lines of input (where the ALT allele
is null). <br>
<br>
Enabling the --allow_non_variant option the lines will be
printed in the VCF output with no consequence data added. <br>
<br>
VEP expects the ALT allele to be null to skip non-variant
lines e.g. <br>
<p><br>
##fileformat=VCFv4.0<br>
#CHROM POS ID REF ALT QUAL FILTER
INFO<br>
22 17181903 var_1 A G . . .<br>
22 17188416 var_2 T . . . .<br>
22 19353405 var_3 G A . . . <br>
</p>
<p>Regards<br>
Helen</p>
<p><br>
</p>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>thanks!</div>
<div>and have a nice weekedn</div>
<div>d</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El vie., 7 jun. 2019 a
las 18:25, Helen Schuilenburg (<<a
href="mailto:helens@ebi.ac.uk" target="_blank"
moz-do-not-send="true">helens@ebi.ac.uk</a>>)
escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi David</p>
<p>Thanks for the information.</p>
<p>The VEP should skip non-variant lines of input by
default and not stop.</p>
<p>We will look at updating the stats to report the
lines skiped.</p>
<p>When using VCF format as input and output, by
default VEP will skip non-variant lines of input.
Please could you try running your sample variants
with vcf output (--vcf) and --allow_non_variant.</p>
<p><a
class="gmail-m_-4451247660575176358gmail-m_-3977281314937812526gmail-m_-8637669723232668235moz-txt-link-freetext"
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt"
target="_blank" moz-do-not-send="true">https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#filt</a><br>
</p>
<p>With the text output, it should also skip the
non-variant lines. VEP could be stopping on your
input file, if it has skipped a number of
non-variant lines. We will look into this</p>
<p>Regards<br>
Helen <br>
</p>
</div>
</blockquote>
</div>
</blockquote>
<br>
</div>
</blockquote>
</div>
</blockquote>
<br>
</body>
</html>