extract unique variant in sample
I have sampleA.vcf and sampleB.vcf I would like to extract the unique variant for each of them normally I would use bedtools like that:
bedtools intersect -v -a sampleA.vcf -b sampleB.vcf > unique_A_variant.vcf
bedtools intersect -v -a sampleB.vcf -b sampleA.vcf > unique_B_variant.vcf
there is other posts suggesting using
Set Difference in VCF Files
How to compare 2 VCF files
GATK selectVarant has an option --discordance
or
SnpSift concordance which will give tab delimited text file (not vcf variant file)
can any one elaborate the difference more because I did not get it will from documentation.
Thanks,
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