Unable to make bed *and* map for convertf
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- Dominant language
- C
- Stars
- 207
- Forks
- 61
- PR merge metrics
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Description
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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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the convertf input preparation described in the issue, including the Perl-generated parameter file and the plink or bcftools steps linked through Biostars. Read the convertf and smartpca input documentation or entry points to determine whether VCF or bed-only input is supported; done means establishing a supported path or documenting the required bed/map inputs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- c, perl
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100