Question: Allelic Depth 1000 Genomes call set
0
gravatar for QVINTVS_FABIVS_MAXIMVS
4.5 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

I'm looking for VCFs that has sample-level allelic depth information.

Something similar to GATK Haplotype Caller. I would like to know the number of reads supporting each SNP per sample.

Is there a VCF file in the 1000 Genomes FTP that contains this information (phase 3 low coverage samples is preferred)

Or did 1000 Genomes not report the allelic depth for the variants? I tried looking around and the only think I could find was a VCF with DP annotation (depth of coverage)

I need the depth of coverage of each allele. I know they phased the genomes so what gives!

1000 genomes ad gatk hc gatk • 1.5k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by QVINTVS_FABIVS_MAXIMVS2.4k

No, you can't get this from 1000g final VCF.

ADD REPLYlink written 4.5 years ago by lh332k

Hmmm. I know the publication releases do not have this information. But there is not any supporting information with allelic depth. Seems odd to be honest (and I work on the structural variation group of 1kG)

ADD REPLYlink written 4.5 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
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