A simple tool for determining whether two BAM files contain reads sequenced from the same sample or patient by counting genotype matches at common SNPs. bam-matcher is most useful at comparing whole-genome-sequencing (WGS), whole-exome-sequencing (WES) and RNA-sequencing (RNA-seq) human data, but can also be customised to compare panel data or non-human data.
There are multiple versions of bam-matcher available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail bam-matcher
To select a module, type
module load bam-matcher/[ver]
where [ver] is the version of choice.
$ module load bam-matcher $ cp -Rp $BAM_MATCHER_HOME/test_data/* . $ bam-matcher.py -B1 sample1.bam -B2 sample2.bam -NC --scratch-dir $(pwd)/$RANDOM --caller freebayes ... ________________________________________ Positions with same genotype: 139 breakdown: hom: 57 het: 82 ________________________________________ Positions with diff genotype: 77 breakdown: BAM 1 | het | hom | subset -------+------+------+------- het | 1 | 0 | 21 | -------+------+------+------- BAM 2 hom | 0 | 12 | - | -------+------+------+------- subset| 43 | - | - | ________________________________________ Total sites compared: 216 Fraction of common: 0.643519 (139/216) ________________________________________ CONCLUSION: LIKELY FROM DIFFERENT SOURCES
Sample session:
$ module load bam-matcher $ bam-matcher.py -B1 sample1.bam -B2 sample2.bam
Create a batch input file (e.g. bam-matcher.sh). For example:
#!/bin/bash module load bam-matcher bam-matcher.py -B1 sample1.bam -B2 sample2.bam
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=1 bam-matcher.sh
Create a swarmfile (e.g. bam-matcher.swarm). For example:
bam-matcher.py -B1 sample1.bam -B2 sample2.bam bam-matcher.py -B1 sample3.bam -B2 sample4.bam bam-matcher.py -B1 sample5.bam -B2 sample6.bam bam-matcher.py -B1 sample7.bam -B2 sample8.bam
Submit this job using the swarm command.
swarm -f bam-matcher.swarm
Once an interactive session is started, the steps are identical to that of Helix (above).