mpileupCounts
This step uses granite mpileupCounts to create a rck file from a bam input file.
This is a pre-requisite step for calling de novo mutations.
- CWL: granite-mpileupCounts.cwl
Requirements
The command takes a bam file and a genome reference fasta file as input.
To optimize performance, it is also possible to specify a file containing a list of genomic regions to parallelize the analysis.
Output
The output rck file contains read pileup counts information for every genomic position, stratified by allele (REFerence vs ALTernate), strand (ForWard vs ReVerse), and type (SNV, INSertion, DELetion).
The rck file is then compressed and indexed with tabix.
A few lines from an example rck file is shown below:
#CHR POS COVERAGE REF_FW REF_RV ALT_FW ALT_RV INS_FW INS_RV DEL_FW DEL_REV
13 1 23 0 0 11 12 0 0 0 0
13 2 35 18 15 1 1 0 0 0 0