modules/biscuit_pileup
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
Description
Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
Input
BAM files to be analyzed. If no tumor_bam file is provided, any number of “normal” BAMs may be provided (“normal” here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
*.{bam}Optional. If a tumor BAM file is provided, pileup will run in “somatic” mode and will annotate variants with their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a tumor BAM file is provided, exactly one normal BAM must be provided.
*.{bam}maintainer
