bam_stat.py¶

Summarize mapping statistics of a BAM or SAM file, including total reads, mapped reads, unique reads, and various alignment categories.

Usage¶

bam_stat.py -i input.bam

Options¶

Option	Description	Default
`-i`, `--input-file`	Alignment file in BAM or SAM format	Required
`-q`, `--mapq`	Minimum mapping quality (phred scaled) to determine "uniquely mapped" reads	30

Output¶

Prints a summary table to stderr with counts for:

Total records, QC failed, PCR duplicates
Unmapped, mapped, paired-end, proper pairs
Read-1, Read-2 counts
Uniquely mapped (based on MAPQ threshold)
Multi-mapped reads (NH tag > 1)
Plus/minus strand reads
Splice reads, non-splice reads

Example¶

$ bam_stat.py -i sample.bam -q 30

#==================================================
#All numbers are READ count
#==================================================

Total records:                          41092
QC failed:                              0
Optical/PCR duplicate:                  0
Non Primary Hits                        8
Unmapped reads:                         0

mapq >= 30 (Uniquely mapped):           41084
mapq < 30 (Multi mapped):              0
Proper-paired reads:                    41084
...