bcftools pipe generated file from first command with second

Question

[cocchi.e89]

It may be silly but I am not getting how to pipe these 2 bcftools commands where I need the file generated by the first command to be an atgument of the second one:

bcftools norm -m -any case.chr21.vcf.gz -Ou | bcftools isec -n~10 case.chr21.altered.vcf.gz

the plain command would be:

bcftools isec -n~10 case.chr21.vcf.gz case.chr21.altered.vcf.gz

I also tried a shell version:

bcftools isec -n~10 <(bcftools norm -m -any case.chr21.vcf.gz -Ou) case.chr21.altered.vcf.gz

but it doesn't work

Thank you so much for any help

Answer 1

[Pierre Lindenbaum]

it will never works. Files for isec must be indexed.

[e0223230]

May I know how to integrate bcftools index in the pipe? I encountered similar issue where I intend to use bcftools index as the second command with inputs from the first command, something like |bcftools index but the |bcftools index command didn't run. Thank you!