recalibrate-BAM automatically uses 1000G indels

[bltsai-UCLA]

--known-sites Mills_and_1000G_gold_standard.indels.hg38.vcf.gz is automatically added to the recalibrate-BAM run command despite me removing bundle_mills_and_1000g_gold_standard_indels_vcf_gz = "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" from the config. We don't want this when aligning to the mouse genome.

config file:
/hot/user/bltsai/projects/JTBRMMEM/metapipeline-DNA/config/recalibrate-BAM.config

working directory:
/hot/user/bltsai/projects/JTBRMMEM/metapipeline-DNA/workdir/44/e9d40b1136141e544b1fc5957e21ff

[zhuchcn]

Seems like the known sites should be provided as a list of VCF files from the config file instead of hard-coded values of those bundle files

[yashpatel6]

This is a requirement for the current setup with recalibrate-BAM where the known sites are specifically coded; I'll transfer the issue there

[yashpatel6]

I do agree the sites should be parameterized a bit better to allow for more flexibility; for a temporary solution, I would suggest something like giving an empty VCF for the mouse runs?