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Thank very much for the quick fix.<br>
<br>
yuan<br>
<br>
Sent from my Huawei Mobile<br>
<br>
-------- Original Message --------<br>
Subject: Re: [ensembl-dev] VEP run on chrY<br>
From: Will McLaren <br>
To: Ensembl developers list <br>
CC: <br>
<br>
<div>
<div dir="ltr">Hi Yuan,
<div><br>
Thanks for reporting this, it's fixed now on release/79, release/80 and release/81. Update ensembl-variation API checkout to get the fix.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 22 July 2015 at 11:41, Yuan Chen <span dir="ltr"><<a href="mailto:yuan@sanger.ac.uk" target="_blank">yuan@sanger.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 style="word-wrap:break-word">The input file :
<div><br>
</div>
<div>
<div>
<div>Y 2657247 . G A 109.291 PASS AA=G;AC=1;AF=0.00081103;AN=1233;DP=5250;NS=1233;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;EAS_AF=0 GT 1 0 0 0 0 0</div>
<div><br>
</div>
<div>/nfs/users/nfs_y/yuan/sanger/src/svn/VEP/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i test1.vcf -offline -dir /data/blastdb/Ensembl/vep -assembly GRCh37 --force_overwrite -vcf<br>
2015-07-22 11:37:58 - Read existing cache info<br>
2015-07-22 11:37:58 - Starting...<br>
2015-07-22 11:37:58 - Detected format of input file as vcf<br>
2015-07-22 11:37:58 - Read 1 variants into buffer<br>
2015-07-22 11:37:58 - Reading transcript data from cache and/or database<br>
[===========================================================================================] [ 100% ]<br>
2015-07-22 11:37:58 - Retrieved 52 transcripts (0 mem, 52 cached, 0 DB, 0 duplicates)<br>
2015-07-22 11:37:58 - Analyzing chromosome Y<br>
2015-07-22 11:37:58 - Analyzing variants<br>
[===========================================================================================] [ 100% ]<br>
2015-07-22 11:37:58 - Calculating consequences<br>
2015-07-22 11:37:58 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)<br>
2015-07-22 11:37:58 - Wrote stats summary to variant_effect_output.txt_summary.html<br>
2015-07-22 11:37:58 - Finished!<br>
farm3-head1[yuan: /g1k-release/20130502/VEP_GENECODE]: m variant_effect_output.txt</div>
<div>##fileformat=VCFv4.0<br>
##VEP=v79 cache=/data/blastdb/Ensembl/vep/homo_sapiens/79_GRCh37 db=.<br>
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|SYMBOL_SOURCE|HGNC_ID"><br>
#CHROM POS ID REF ALT QUAL FILTER INFO<br>
Y 2657247 . G A 109.291 PASS AA=G;AC=1;AF=0.00081103;AN=1233;DP=5250;NS=1233;AMR_AF=0.0029;AFR_AF=0;EUR_AF=0;SAS_AF=0;EAS_AF=0;CSQ=A|upstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000534739|protein_coding|||||||||||1603|-1|HGNC|11311,A|upstream_gene_variant|MODIFIER|RNASEH2CP1|ENSG00000237659|Transcript|ENST00000454281|processed_pseudogene|||||||||||621|1|HGNC|24117,A|upstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000525526|protein_coding|||||||||||1603|-1|HGNC|11311,A|downstream_gene_variant|MODIFIER|RNU6-1334P|ENSG00000251841|Transcript|ENST00000516032|snRNA|||||||||||4353|1|HGNC|48297,A|upstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000383070|protein_coding|||||||||||1507|-1|HGNC|11311 GT
1 . . . . .</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>yuan</div>
</font></span>
<div>
<div class="h5">
<div><br>
</div>
<div>On 22 Jul 2015, at 11:00, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">Hi Yuan,
<div><br>
VEP shouldn't change the genotype data in your VCF file, can you provide a sample of input and a command that recreates the issue?</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 22 July 2015 at 09:41, Yuan Chen <span dir="ltr"><<a href="mailto:yuan@sanger.ac.uk" target="_blank">yuan@sanger.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
Hi Will,<br>
<br>
When I run VEP (79 version) on chrY which has genotype 0 or 1 in vcf file (i.e not 0/0), the VEP output file changed all 0 to '.', is this expected ?<br>
<br>
yuan<br>
<br>
Sent from my Huawei Mobile<br>
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