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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 $conv_fh 'familynames: NO';
but the requirement for having both a bed and a map file is really blocking me from moving on.
Is there some other way that I can run convertf with a VCF, or bed alone, as input to convertf to get the input for smartpca?
Thanks for your help
The text was updated successfully, but these errors were encountered:
I’m trying to run convertf in the process of running smartpca. However, in the process of preparing files for convertf, I’m getting bizarre errors from plink and/or bcftools that are not getting any answers on online forums or GitHub: https://www.biostars.org/p/9531207/
I make the input file for convertf in perl:
my ($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
The text was updated successfully, but these errors were encountered: