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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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Population level caling: Genotype Step concept & Merging step #163

Closed nitha26 closed 2 years ago

nitha26 commented 2 years ago

Hi @brentp could you please explain 1. how this #160 squaring concept is applied in population level or when we don't use trios (I understand squaring concept in trios)?

  1. And how can I filter out only PASS variants from end VCF file (completion of all steps in population level calling) ? could you help me to filter out PASS variants for next level analysis?

  2. Whether smoove support genotyping of other tools SVs VCF file (Manta VCF, GRIDSS VCF)?

  3. Can smoove do merging step for creating consensus file? eg (Delly VCF + smoove VCF = ConsensusSVcall?

Thanks a lot!

brentp commented 2 years ago

Hi,

  1. I have explained this as best I can. This is commonly done for SNPs and indels as well as for SVs.
  2. you can use bcftools to do this type of filtering.
  3. no
  4. no