converting plink's bed files to snppit input?

eriqande / snppit

Program for large scale parent pair inference (in salmon, etc.)

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converting plink's bed files to snppit input? #6

Closed ckastall closed 4 months ago

ckastall commented 1 year ago

Is there by any chance a script or tool available to quickly prepare snppit input file? For instance, when starting from a VCF file or plink's bed (+fam +bim) files?

Plink's bed file format: https://www.cog-genomics.org/plink/1.9/formats#bed

Thank you

eriqande commented 4 months ago

Hey ckastall,

sorry I missed this until now.

I don't have a script for that. I would plink recode the bed file into a text based ped file and then use awk.

If coming from a VCF file I would use bcftools query to extract everything into a decent text representation of the genotypes and then use awk or R to transpose, as needed.

Cheers,

eric