<div dir="ltr"><div><div><div>hi will, <br>i produced a couple of files with only 1000 lines. <br>the error is in my samtools vcf files i have "variants" that differ in the number of Ns for ref and alt alleles. <br>
</div>and these are correctly omitted by VEP. <br></div>sorry to have bothered you with my problem!<br><br></div>regards marlies <br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-04-28 11:49 GMT+02:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I can't think of anything else - perhaps you can send me a snippet of your input that recreates the problem?<div>
<br></div><div>e.g. a file with 1000 lines that the VEP reports annotating only 995</div><span class="HOEnZb"><font color="#888888"><div>
<br></div><div>Will</div></font></span></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div class="">On 28 April 2014 10:01, Marlies Dolezal <span dir="ltr"><<a href="mailto:marlies.dolezal@gmail.com" target="_blank">marlies.dolezal@gmail.com</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div class="">hi Will,<br>thanks for your quick reply!<br>unfortunately using the --allow_non_variant option gave the exact same output. <br>
<br><br>-offline --allow_non_variant --force_overwrite --species bos_taurus --fork 16 - --input_file Chr$i.vcf --o Chr$i.vep<br>
<br>Start time 2014-04-28 10:27:05<br>End time 2014-04-28 10:36:57<br>Run time 592 seconds</div><div><br><br><br><div class="">Lines of input read 900857<br>Variants processed 900241<br></div></div><div class="">Variants remaining after filtering 900241<br>
<br><br></div></div><div class="">any other ideas?<br>
thanks again!<br>regards, marlies <br></div><div><div class=""><br><br>2014-04-28 10:24 GMT+02:00 Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>>:</div><div><div><br>><div><div class="h5">
<br>> Hello,<br>><br>
> It's possible you have some non-variant lines in your VCF; these will have a "." as the ALT allele column, something like:<br>
><br>> 21 26960070 . G . . . .<br>><br>> By default the VEP ignores these. You can force the VEP to allow them through (though they still won't be annotated) using --allow_non_variant.<br>
><br>> Regards<br>><br>> Will McLaren<br>> Ensembl Variation<br>><br>><br>> On 28 April 2014 08:52, Marlies Dolezal <<a href="mailto:marlies.dolezal@gmail.com" target="_blank">marlies.dolezal@gmail.com</a>> wrote:<br>
>><br>>> hi all,<br>>><br>>> i am using the latest VEP version 75 (API)(75) to annotate samtools VCF files.<br>>><br>>> -offline --force_overwrite --species bos_taurus --fork 16 --input_file Chr$i.vcf --o Chr$i.vep<br>
>><br>>><br>>> the General statistics section of the VEP_summary.html tells me that all lines of my vcfs are read in, but only a subset of these are processed.<br>>> eg:<br>>> Lines of input read 900857<br>
>> Variants processed 900241<br>>><br>>> the difference in lines does not correspond to header/comment lines only.<br>>><br>>> where can i find out which variants are not processed to try to figure out why they are not processed?<br>
>><br>>> thanks a lot in advance<br>>> regards Marlies<br>>><br>>><br>>><br>>><br>>><br>>><br>>> --<br>>> Dr. Marlies Dolezal<br>>> 1030 Vienna<br>>> Austria/Europe<br>
>><br>>> marlies.dolezal(at)<a href="http://gmail.com" target="_blank">gmail.com</a><br>>><br>>> “The great tragedy of science is the slaying of a beautiful hypothesis by an ugly fact.”<br>>> Thomas Henry Huxley<br>
>> (1825-1895)<br>>><br>>><br>>><br>>><br>>> _______________________________________________<br>>> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
>> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
>> Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>>><br>><br>><br>> _______________________________________________<br>> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>> Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
><br><br><br><br>--<br>Dr. Marlies Dolezal<br>1030 Vienna<br>Austria/Europe<br><br>marlies.dolezal(at)<a href="http://gmail.com" target="_blank">gmail.com</a><br><br>“The great tragedy of science is the slaying of a beautiful hypothesis by an ugly fact.”<br>
Thomas Henry Huxley<br>(1825-1895)</div></div></div></div></div></div><div><div class="h5">
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<br></blockquote></div><br><br clear="all"><br>-- <br>Dr. Marlies Dolezal<br>1030 Vienna <br>Austria/Europe<br><br>marlies.dolezal(at)<a href="http://gmail.com" target="_blank">gmail.com</a><br><br>“The great tragedy of science is the slaying of a beautiful hypothesis by an ugly fact.”<br>
Thomas Henry Huxley<br>(1825-1895)<br><br>
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