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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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bcftools isec support for a --file-list? #2092

Closed jhampstead closed 5 months ago

jhampstead commented 5 months ago

I'm using bcftools to preprocess VCFs before running relationship inference using KING. I'm using bcftools isec to create a set of useful SNPs for this purpose on more than 70,000 individuals.

However, in my current script bcftools isec is crashing with the error that the argument list is too long. I've checked my system's ARG_MAX and it's terabytes of memory in size, so I'm wondering if this issue stems from bcftools?

An easy workaround for me would be the addition of a --file-list argument to bcftools isec, with exactly the same functionality as the --file-list argument that already exists for bcftools merge. If this is impossible (or difficult), are there any other workarounds you might suggest? It's possible the error is coming from my system and there's something I haven't checked. Thanks!

pd3 commented 5 months ago

I added the -l, --file-list option to get the list of file names from a file. I hope this helps