Question: Vcf-compare two multi-sample vcf files
1
gravatar for ApoorvaB
22 months ago by
ApoorvaB170
United States
ApoorvaB170 wrote:

Hi,

I have two large multi-sample vcf files. The samples in both files are the same except the snp's were called using different programs. i want to see if they match. I am not sure if vcf-compare works. I gave it a shot and it returned all zeros. Is there any other way i can compare two multi-sample vcf files?

Thanks

vcf-compare vcftools • 1.3k views
ADD COMMENTlink modified 13 months ago by maduh1710 • written 22 months ago by ApoorvaB170
1
gravatar for Pierre Lindenbaum
22 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

Is there any other way i can compare two multi-sample vcf files?

you could use picard/GenotypeConcordance

Evaluate genotype concordance between callsets.This tool evaluates the concordance between genotype calls for samples in different callsets where one is being considered as the truth (aka standard, or reference) and the other as the call that is being evaluated for accuracy.

java -jar picard.jar GenotypeConcordance \
      CALL_VCF=input.vcf \
      CALL_SAMPLE=sample_name \
      O=gc_concordance.vcf \
      TRUTH_VCF=truth_set.vcf \
      TRUTH_SAMPLE=truth_sample#
ADD COMMENTlink written 22 months ago by Pierre Lindenbaum116k
0
gravatar for maduh17
13 months ago by
maduh1710
Kuala Lumpur, Malaysia
maduh1710 wrote:

!!!!!!!!!!!!!!!!! I found a link saying that GATK's GenotypeConcordance is being outphased: https://gatkforums.broadinstitute.org/gatk/discussion/5795/genotype-concordance-output

So might wanna just use picard as Pierre suggested

ADD COMMENTlink written 13 months ago by maduh1710
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