TSV with multi-allelic sites to VCF

Question

[Christian]

Dear all,

I am trying to convert a TSV output of some tools to a valid VCF. This is what a sample of the file looks like:

mutID   Chr Position    Ref Alt nANNO   N_eps   N_PSI   tAD
474 chr2    50282084    GT  G   mappable    0.293935566 0   11
551 chr2    128180742   A   C   mappable    0.293935566 0   141
2406    chr12   49426729    AGCTGCT A   mappable    0.174180946 0   24

Bcftools convert has utilities for tsv2vcf conversion (here), but "insertions and deletions are not supported yet". Clearly, I should either discard or preferably break multi-allelic sites first. The preferred way to do this, bcftools norm -m-both only accepts VCF files as input.

I was not able to find any other utilities or code snippets that can address this problem. As always, I would appreciate any insight.

Best

Christian

[Pierre Lindenbaum]

it's not clear whether you want to remove multi-allelic sites first from your TSV file or something else.

[Christian]

Apologies. In short, I want to convert a TSV file with multi-allelic sites to VCF.

If possible, I would prefer to split multi-allelic sites in the TSV (as bcftools norm would do for VCF) instead of removing them. If that's not possible, I would want to remove multi-allelic sites first from my TSV file, yes.

[barslmn]

I have created a tutorial about converting tsv to vcf a few months earlier that might be used as a guide. Converting TSV file to VCF You can do other manipulations after converting to vcf file with bcftools.