bam_tumor_only_somatic_variant_calling_gatk
Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.
Description
Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering.
Input
list containing one BAM file indexe, also able to take CRAM index as an input
[ *.{bam.bai/cram.crai} ]
Population vcf of germline sequencing, containing allele fractions.
*.vcf.gz