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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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feature requests for output VCF #109

Open zeeev opened 9 months ago

zeeev commented 9 months ago

Hello,

A few requests regarding the output VCF.

  1. It would be really useful if the REF/ALT alleles could be populated via the graph traversal. Most users won't know how to walk the graph to extract the alleles.
  2. Replacing genotype separator to | or /, rather than :.
  3. It appears that the sample names on the final step is ignored, the VCF samples still has the samples as {sample}_{hap1/2} rather than {sample} which is what is encoded in sample_names.txt
./k8 mgutils-es6.js merge2vcf -r0 merged_sv_calls_labeled.bed -s sample_names.txt
lh3 commented 7 months ago
  1. Will add later
  2. Minigraph only outputs haplotype and thus GT only has one number. : is not for separating haplotypes; it separates GT and GT0.
  3. Could you show an example?