The pileup functionality goes through a BAM file and for every position provides a string of bases covering that position and the genotype likelihoods. If a post-mortem damage pattern or a base quality score recalibration table is provided it will be taken into account in the genotype likelihoods. See estimatePMD for more information on how to produce a post-mortem damage pattern and BQSR or recal for more information on how to produce a base quality score recalibration table.
- A BAM file
- optional: post-mortem damage pattern
- optional: base quality score recalibration tables
- A table called example_pileup.txt containing for each genomic position the sequencing depth, the identity of the bases covering it and the genotype likelihoods (taking into account potential PMD and recalibration parameters).
./atlas task=pileup bam=example.bam BQSRQuality=example_BQSR_ReadGroup_Quality_Table.txt pmdFile=example_PMD_input_Empiric.txt
- printOnlySitesWithData: Only print sites with data. Default = false