slivar rare-disease

[brentp]

most people will run the rare-disease pipeline as-is. this can be made faster an easier with an interface like:

slivar rare-disease \
   --min-depth 10 \
   --ab 0.2 \ 
   --min-gq 20 \
   --impactful \ # or --genic
   -g gnomad.v2.hg38.zip \
   --dominant-af 0.001 \ # de novo, autosomal dominant
   --recessive-af 0.01 \ # recessive, comphet
   --prefix $cohort \
   --ped $ped_file \
   --vcf $vcf

with many of those as defaults, so it would look like:

slivar rare-disease \
    -g gnomad.v2.hg38.zip \
    --prefix $cohort \
    --ped $ped_file \
    --vcf $vcf

this will output the vcf(s) and the final tsv from slivar tsv.

[nicholas-owen]

is this something being implemented into slivar ?

[brentp]

that's the plan, but I have not even started the implementation. For now, follow the rare-disease wiki page.