8000 Add default support for haploid variant calls · Issue #596 · nf-core/raredisease · GitHub
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Add default support for haploid variant calls #596

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jemten opened this issue Aug 14, 2024 · 2 comments
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Add default support for haploid variant calls #596

jemten opened this issue Aug 14, 2024 · 2 comments
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enhancement Improvement for existing functionality

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@jemten
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jemten commented Aug 14, 2024

Description of feature

Deepvariant version 1.6.1 has support for haploid calls on the X and Y chromosome for males, https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-haploid-support.md.

We could add the PAR region file as an optional input to be passed to the module and update the config for deepvariant to by default include the --haploid_contigs parameter for males.

Could something like this:

        ext.args = { [
            "--model_type=${params.analysis_type.toUpperCase()}",
            (meta.sex == 1 ) ? ( (params.genome == 'GRCh37') ? '--haploid_contigs="X,Y"' : '--haploid_contigs="chrX,chrY"' ) ) : ''
        ].join(' ')}

I'm sure that there is a more elegant way of doing it 😆
@jemten jemten added the enhancement Improvement for existing functionality label Aug 14, 2024
@fellen31
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I forgot to add --par_regions_bed with the 1.6.1 module update, (added in nf-core/modules#6022 yesterday), so the module in raredisease needs to be updated again.

@ramprasadn
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Added in #598

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@jemten @ramprasadn @fellen31
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