Question: bcftools pipe generated file from first command with second
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cocchi.e89 • 120 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
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modified 8 months ago
by
Pierre Lindenbaum ♦ 133k
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written
8 months ago by
cocchi.e89 • 120
