Question: bcftools pipe generated file from first command with second
gravatar for cocchi.e89
8 months ago by
cocchi.e89120 wrote:

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

pipe bcftools vcf • 298 views
ADD COMMENTlink modified 8 months ago by Pierre Lindenbaum133k • written 8 months ago by cocchi.e89120
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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

ADD COMMENTlink written 8 months ago by Pierre Lindenbaum133k
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