Vcf-compare two multi-sample vcf files

Question

[AB]

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

Answer 1

[Pierre Lindenbaum]

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#

Answer 2

[maduh17]

!!!!!!!!!!!!!!!!! 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