Recipe for RNA haplotypecaller, resolves #484 #501
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| say {$FILEHANDLE} q{## GATK HaplotypeCaller}; | ||
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| my $pcr_indel_model; | ||
| if ( $active_parameter_href->{gatk_haplotypecaller_pcr_indel_model} ) { |
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Why do you need this if condition? Will the result not be the same with:
my $pcr_indel_model = $active_parameter_href->{gatk_haplotypecaller_pcr_indel_model}
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True we don't need it. It was a remain from the rare disease haplotypecaller recipe
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| my $pcr_indel_model; | ||
| if ( $active_parameter_href->{gatk_haplotypecaller_pcr_indel_model} ) { | ||
| ## Set to GATK default (CONSERVATIVE) for RNA-seq |
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'##' Should be set to GATK default (CONSERVATIVE) for RNA-seq
Maybe we should add a check either FATAL or WARN that this is so in the sanity check part of MAIN::Analyse
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Possibly. The ## statement I wrote was perhaps more assertive than I ment it to be. CONSERVATIVE is GATK default when running haplotypecaller but I'm not entirely sure that it is the optimal model. Kind of depends on the prep and quality of the RNA I guess. We use NONE for the PCR free wgs libraries
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