<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>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>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">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">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">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>
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