4.2 BAMDiagnostics
Estimating approximate depth, read length frequencies and mapping quality frequencies
BAMDiagnostics provides a set of read statistics for the input BAM file while taking into account all standard input filters. The output are written to .txt files that summarize the following information:
- Total number of reads
- Number of reads that passed filters
- Number of duplicate reads
- Average read length
- Maximum read length
- Number of proper pairs
- Average fragment length (only known for paired-end data)
- Total number of soft-clipped positions
- Average soft-clipped length
- Average aligned length
- Mean sequencing depth across the whole genome
- Average mapping quality
It also provides histograms which display the distributions of fragment lengths, mapping qualities, read lengths, soft-clipped lengths and aligned lengths. All of this data is written for all read groups combined, as well as for each read group separately.
4.2.1 Parameters
4.2.1.2 Specific Parameters
--perChromosome |
Output data per chromosome into a *_diagnostics.txt diagnostics file. |
--printReferenceLength |
Print reference lengths of chromosomes to file. |
--identifyDuplicates |
Create file of pairs of reads which are potentially duplicates. |
--writeMates |
Write seperate output for first and second mate. |
4.2.2 Output
| *_fragmentLengthHistogram.txt | Counts for all fragment length for all read groups combined and individual read groups. |
| *_mappingQualityHistogram.txt | Mapping quality counts for all read groups combined and individual read groups. |
| *_readLengthHistogram.txt | Read length counts for all read groups combined and individual read groups. |
| *_softClippedLengthHistogram.txt | Length of soft-clipped bases as counts for all read groups combined and individual read groups. |
| *_alignedLengthHistogram.txt | Aligned length counts for all read groups combined and individual read groups |
| *_potentialDuplicates.txt.gz | List of pairs of reads which are potentially duplicates. |
| *_diagnostics.txt | File containing per-read group summary statistics. Also contains per chromosome summary statistics is provided when --diagnosticsPerChromosome parameter is used. This file can be used as input file for the mergeOverlappingReads task. |