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HurlesGroupSanger / indelible

Structural Variation breakpoint discovery via adaptive learning
GNU General Public License v3.0
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InDelible VCF Format #6

Open eugenegardner opened 3 years ago

eugenegardner commented 3 years ago

Hey Eugene,

every step ran smoothly now and I get a tsv in the end, now I am trying to do the complete run. I was also wondering about a vcf as output, is there any method to produce that?

Originally posted by @marrip in https://github.com/eugenegardner/indelible/issues/4#issuecomment-826845356

eugenegardner commented 3 years ago

InDelible does not currently have a VCF format output. If this becomes something that more and more users want I can look into creating it.

This was decided mostly because:

  1. We only supply breakpoints rather than complete REF/ALT sequence.
  2. We don't genotype breakpoints in the strict sense so almost all genotypes would be missing ("./.")
  3. The small number of variants that we identified in DDD means it wasn't really necessary for reporting back to patients/clinicians.
  4. Most variants of interest are present in only one individual and generating a large file consisting mostly of "0" genotypes didn't make sense.

An overview of your use-case might help me in seeing if VCF might be useful for more people (i.e. if more people are using it as a population-level variant caller...).

marrip commented 3 years ago

Hey,

I understand your reasoning and it's not so urgent for me with a vcf. 😃