Question: Meaning of "EX_TARGET" in VCF files 1000 genomes
0
gravatar for GabrielMontenegro
2.5 years ago by
United Kingdom
GabrielMontenegro540 wrote:

I am working with some 1KG VCF files and I just extracted biallelic SNPs using the vcflib library. However, I noticed that some SNPs have this additionally field: "EX_TARGET"

...SAS_AF=0.001;VT=SNP;EX_TARGET    GT  0|0 0|0...

I've googled it and however I haven't found it anywhere on the 1KG documentation. I just found one website that mentioned these were not reliable? What does it mean? Are these only SNPs on exons?

vcf genome • 966 views
ADD COMMENTlink modified 2.5 years ago by Pierre Lindenbaum124k • written 2.5 years ago by GabrielMontenegro540
3
gravatar for Pierre Lindenbaum
2.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:
 curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | gunzip -c | grep "EX_TARGET"  -m1
##INFO=<ID=EX_TARGET,Number=0,Type=Flag,Description="indicates whether="" a="" variant="" is="" within="" the="" exon="" pull="" down="" target="" boundaries"="">

indicates whether a variant is within the exon pull down target boundaries

ADD COMMENTlink written 2.5 years ago by Pierre Lindenbaum124k
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