locus ID regex pattern when column has colons about gbs_snp_filter HOT 5 CLOSED

Hi Quinn,

Really having to rack my memory here, but I think unfortunately the ":" limitation comes through with the use of PLINK by the package downstream (it is the one that can't handle colons in the name). Could you post a couple of lines of the #CHROM POS ID columns here? That might help us plan a solution!

Cheers,

Alana

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Hi Alana,

Thanks for your help! Attached is the first few lines of my vcf file (only the first 3 columns). I've thinned my vcf file with plink previously and haven't had problems. I'm primarily interested in the HWE filtering and using this script to filter out loci that are out of HWE in each of the 4 populations (per Pearman et al. (2022) - Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data).

Thanks!

chrm_loci_populations.snps.txt

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Hi Quin,

Cool - to me it looks like your ID column is going to be unique even if everything following the first ':' is stripped away (based on this wee sample size). If you are worried that that might not be the case (i.e. you might have multiple sites that start with the same number), an option would be to run some kind of regex find and replace, and substitute something like an underscore for the colon. Can you test out and see whether the scripts work OK for you? (hopefully no other bugs pop up!). If it does, I will tweak the README to say you can have colons, but anything before the colon needs to be unique.

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Great, thanks! I filtered to have a single snp per locus, so they should all be unique (that may not be the case for those who kept multiple snps per locus). The script worked, although I added :.* to the 8th line because I kept getting an error saying my GBS_SNP_filter.txt file didn't have 8 lines. Thank you for your help!

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Thanks Quinn - sorry about this slow response - I'll close the issue and add that workaround to the readme.

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