bam_variant_calling_mpileup_bcftools
Subworkflow to compute genotype likelihoods from BAM files using
bcftools/mpileup and bcftools/call variants by chromosomes.
The resulting VCF files are then merged by chromosomes and
annotated with bcftools/annotate to give an ID for each variants.
During samples merging and region concatenation, all metadata will
be preserved and stored in the key metas at each step.
Description
Subworkflow to compute genotype likelihoods from BAM files using
bcftools/mpileup and bcftools/call variants by chromosomes.
The resulting VCF files are then merged by chromosomes and
annotated with bcftools/annotate to give an ID for each variants.
During samples merging and region concatenation, all metadata will
be preserved and stored in the key metas at each step.
Input
List of keys that define the sample.
All file sharing the same values for these keys will be merged together.
e.g. [ “id” ]
Shared value that will be set to meta_sample_merge_key for all samples to be merged together.
e.g. “all_samples”
List of keys to be used to gather the VCF files by region with vcf_gather_bcftools.
All file sharing the same values for these keys will be gathered together.
e.g. [ “id”, “panel_id” ]
Whether to sort the VCF files by region after concatenation with
vcf_gather_bcftools.
included modules and subworkflows
maintainer
