Hi, I attempted to find overlapping variants across my four panels using
bcftools isec -p dir -n=4 <file1.vcf.gz> <file2.vcf.gz> <file3.vcf.gz> <file4.vcf.gz>
I got this list of outputs:
0000.vcf 0001.vcf 0002.vcf 0003.vcf README.txt sites.txt
Where the README.txt says:
dir/0000.vcf for stripped <file1.vcf.gz> dir/0001.vcf for stripped <file2.vcf.gz> dir/0002.vcf for stripped <file3.vcf.gz> dir/0003.vcf for stripped <file4.vcf.gz>
My questions are— 1) what does “for stripped” mean? 2) Is sites.txt the list of overlapping variants across the four panels? I’ve searched for documentation that explains the outputs but haven’t been successful. Thanks for your help!