Entering edit mode
2.2 years ago
JellyFrog
▴
10
What I expect to get: FMT/DP>40 from VCFs of two samples, and check sample identity, gives percentages or something.
What I have tried:
bcftools query -i'FMT/DP>40' -f '%CHROM\t%POS\t%REF\t%ALT\t%FORMAT\n' sample1.vcf.gz > sample1.txt
bcftools query -i'FMT/DP>40' -f '%CHROM\t%POS\t%REF\t%ALT\t%FORMAT\n' sample2.vcf.gz > sample2.txt
Then I used gtcheck to check sample identity
bcftools gtcheck -g sample1.txt sample2.txt
My question is:
It seems gtcheck can't compare two TXT files. I also tried output samples in the first chunk to vcf.gz but it still doesn't work.
Any help is appreciated.
