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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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smoove/paste + singularty + 1185 vcfs: argument list too long #151

Closed lindenb closed 3 years ago

lindenb commented 3 years ago

Hi @brentp

I'm trying to use smoove/paste with singularity and 1185 bams. I got an error

argument list too long

it's not clear to me if the problem comes from bash/singularity/smoove.

1) is it possible to use a divide-and-conquer strategy with paste ? : paste vcfs 1-100, paste vcfs 101-200, paste vcfs 201-300, etc... and then paste the merged vcfs ?

2) Am I wrong ? smoove doesn't support a .list extension like you did here : https://github.com/brentp/somalier/issues/37#issuecomment-550502468 ?

thank you again for your help :-)

lindenb commented 3 years ago

answering my own question: using a divide-and-conquer strategy worked. (however I'm not sure if the INFO fields were correctly merged).

brentp commented 3 years ago

Hi Pierre, yes, I should add support for a .list argument here. Would love to get a PR to that effect. Otherwise, I'll leave this open til I have a chance to implement.

brentp commented 3 years ago

Hi Pierre, I wonder if using bcftools merge with -m none makes it faster?