extract unique variant in sample
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Entering edit mode
7.2 years ago
Medhat 9.7k

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,

SNP next-gen • 1.2k views
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