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ATLAS / Diagnostics: pileup


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).

Usage Example

./atlas task=pileup bam=example.bam BQSRQuality=example_BQSR_ReadGroup_Quality_Table.txt pmdFile=example_PMD_input_Empiric.txt

Specific Arguments

  • printOnlySitesWithData: Only print sites with data. Default = false