Interpreting bcftools isec output

1

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!


bcftools


isec


intersection


vcf

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