[ensembl-dev] VEP run on chrY

[Yuan Chen]

Thank very much for the quick fix.

yuan

Sent from my Huawei Mobile

-------- Original Message --------
Subject: Re: [ensembl-dev] VEP run on chrY
From: Will McLaren
To: Ensembl developers list
CC:

Hi Yuan,

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.

Will

On 22 July 2015 at 11:41, Yuan Chen <yuan at sanger.ac.uk<mailto:yuan at sanger.ac.uk>> wrote:
The input file :

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

/nfs/users/nfs_y/yuan/sanger/src/svn/VEP/variant_effect_predictor.pl<http://variant_effect_predictor.pl> -i test1.vcf -offline -dir /data/blastdb/Ensembl/vep -assembly GRCh37 --force_overwrite -vcf
2015-07-22 11:37:58 - Read existing cache info
2015-07-22 11:37:58 - Starting...
2015-07-22 11:37:58 - Detected format of input file as vcf
2015-07-22 11:37:58 - Read 1 variants into buffer
2015-07-22 11:37:58 - Reading transcript data from cache and/or database
[===========================================================================================]  [ 100% ]
2015-07-22 11:37:58 - Retrieved 52 transcripts (0 mem, 52 cached, 0 DB, 0 duplicates)
2015-07-22 11:37:58 - Analyzing chromosome Y
2015-07-22 11:37:58 - Analyzing variants
[===========================================================================================]  [ 100% ]
2015-07-22 11:37:58 - Calculating consequences
2015-07-22 11:37:58 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)
2015-07-22 11:37:58 - Wrote stats summary to variant_effect_output.txt_summary.html
2015-07-22 11:37:58 - Finished!
farm3-head1[yuan: /g1k-release/20130502/VEP_GENECODE]: m variant_effect_output.txt
##fileformat=VCFv4.0
##VEP=v79 cache=/data/blastdb/Ensembl/vep/homo_sapiens/79_GRCh37 db=.
##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">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
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       .       .       .       .       .

yuan

On 22 Jul 2015, at 11:00, Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>> wrote:

Hi Yuan,

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?

Regards

Will

On 22 July 2015 at 09:41, Yuan Chen <yuan at sanger.ac.uk<mailto:yuan at sanger.ac.uk>> wrote:
Hi Will,

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 ?

yuan

Sent from my Huawei Mobile
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