5.8 pileup
Printing pileup from BAM file
pileup goes through the input BAM file and for every position provides a string of bases covering that position and the genotype likelihoods while taking into account all standard input filters. If a post-mortem damage pattern or a base quality score recalibration table is provided, these will be taken into account in the estimated genotype likelihoods. See PMD for more information on how to produce a post-mortem damage pattern, and BQSR for more information on how to produce a base quality score recalibration table.
5.8.1 Input
Required inputs :
--bam Input_bam_file.bam |
Input bam file |
Optional inputs :
--pmd Input_PMD.txt |
post-mortem damage parameters (see PMD for generating such a file) |
--recal recal.txt |
quality score recalibration file (see recal) |
Specific Parameters :
--printAll |
print all sites that pass filters, including those without data. By default, only sites with data will be printed. |
--histograms |
print the counts for following histogram parameters: Sequencing depth (depth), Base qualities (qualities), Base contexts (contexts), Allelic depth (allelicDepth) |
--onlyHistograms |
only write histogram files |
5.8.2 Output
| *_pileup.txt.gz | Text file containing for each genomic position the sequencing depth, identity of the bases covering it and the genotype likelihoods (taking into account potential PMD and recalibration parameters, when provided.) |
| *_depthPerChromosome.txt.gz | |
| *_depthPerWindow.txt.gz | |
| *_allelicDepth.txt.gz (optional) | only produced when --histograms argument is used. |
| *_contextInformation.txt.gz (optional) | only produced when --histograms argument is used |
| *_depthPerSiteHistogram.txt.gz (optional) | only produced when --histograms argument is used |
| *_qualHistogram.txt.gz (optional) | only produced when --histograms argument is used |
| *_filterSummary.txt | Filter summary for all read groups combined and individual read groups. |