Question: Gatk Mutli-Samples Vcf
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gravatar for huskerjeff492
5.5 years ago by
huskerjeff492160
huskerjeff492160 wrote:

I called the variants for 5 samples with Unified Genotyper/GATK. One of the samples has a mutation that is causing disease but the vcf output from the UG looks like chrM 12015 . C T 818.19 . AC=2;AF=0.071;AN=28;BaseQRankSum=-1.570;DP=511;Dels=0.00;FS=3.861;HaplotypeScore=0.4205;InbreedingCoeff=0.9977;MLEAC=2;MLEAF=0.071;MQ=58.89;MQ0=0;MQRankSum=0.152;QD=32.73;ReadPosRankSum=0.959 GT:AD:DP:GQ:PL 0/0:16,0:16:42:0,42,510 0/0:17,0:17:45:0,45,568 0/0:24,0:24:72:0,72,854 0/0:149,0:149:99:0,418,5048 0/0:36,0:36:96:0,96,1193 0/0:18,0:18:51:0,51,611

As you can tell the vcf has the analysis for all variants but I am looking for a variant that is present in just 1 of the 5 samples.

What tool am I missing that tells me this variant is present in one sample but not the other 4?

Thanks for the help

I don't think I asked my question correctly.

let my rephase.

If I had three vcf files one mother one father and one child I could simply use vcftools to find any variants in the child vcf but not in the parents vcf files. However I was following GATK best practice and called a family all together. So is there tool out there people use do analyze a mutli-sample vcf to do this same analysis, my analysis is not tio but a family.

I could write a script that looks at the GT field and anywhere parents were 0/0 but child was 1/0 , I could pull out this denovo candidate but there has to be a tools that is in common use for this.

I hope that clarifies my question.

vcf gatk • 2.4k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by huskerjeff492160
0
gravatar for Pierre Lindenbaum
5.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Pierre Lindenbaum118k
0
gravatar for Alex Paciorkowski
5.5 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

See Select certain column from vcf file

You can write a script in the language of your choice and pull out the column you are interested in as 0/1 where the others are 0/0.

ADD COMMENTlink written 5.5 years ago by Alex Paciorkowski3.3k
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