[ensembl-dev] VEP run on chrY

[Will McLaren]

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> 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 -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> 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> 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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