bcftools sec for multiple files

Question

[evelyn]

Hello,

I am comparing five vcf files each with multiple samples using bcftools isec:

bcftools isec -p dir -n=5 a.vcf.gz b.vcf.gz c.vcf.gz d.vcf.gz e.vcf.gz

It results in these files:

0000.vcf  0001.vcf  0002.vcf  0003.vcf  0004.vcf  README.txt  sites.txt

However, the output does not show intersection sites among all five vcf files. I am not sure if something is wrong in the command line. I will appreciate any suggestions. Thank you.

Answer 1

[onestop_data]

Please see this How bcftools isec works ? . why do you have -n=5 and not 7 if you have 7 files?

[evelyn]

Hello @metageni,

I have corrected the question as I have five files. I have already read the post you mentioned but I am still not sure which is the intersection file for all the combinations as the header looks the same for all output files. Thank you!