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Unable to make bed *and* map for convertf #80

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hhg7 opened this issue Jul 19, 2022 · 0 comments
Open

Unable to make bed *and* map for convertf #80

hhg7 opened this issue Jul 19, 2022 · 0 comments

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@hhg7
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hhg7 commented Jul 19, 2022

I’m trying to run convertf in the process of running smartpca. However, in the process of preparing files for convertf, I’m getting bizarre errors from plink and/or bcftools that are not getting any answers on online forums or GitHub: https://www.biostars.org/p/9531207/

I make the input file for convertf in perl:

my ($conv_fh, $convert_params_filename) = tempfile(DIR => '.', UNLINK => 0);
say $conv_fh "genotypename: $out_stem.bed";
say $conv_fh "snpname: $out_stem.map";
say $conv_fh "indivname: $fam_file";
say $conv_fh "outputformat: PACKEDANCESTRYMAP";
say $conv_fh "genotypeoutname: $out_stem.geno";
say $conv_fh "snpoutname: $out_stem.snp";
say $conv_fh "indivoutname: $out_stem.ind";
say $conv_fh 'familynames: NO';

but the requirement for having both a bed and a map file is really blocking me from moving on.

Is there some other way that I can run convertf with a VCF, or bed alone, as input to convertf to get the input for smartpca?

Thanks for your help

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