Count reads in each intervals from a bed file. Reads are stored in bam file. pyCoverage is similar to coverageBed with -counts and -b bam_file.
But pyCoverage can use multiple process and the run very fast.
Run pyCoverage using 8 threads:
pyCoverage.py bam_sorted.bam interval.bed 8 > interval.cov
The counts are added to the end of each line in interval.bed.
pyCoverage.py accept stdin:
awk '$1==4' interval.bed | pyCoverage.py bam_sorted.bam - 16 > interval_chr4.cov
Bam file must be sorted and indexed.
pyCoverage will use 40 threads if the threads number is not specified:
pyCoverage.py bam_sorted.bam interval.bed > interval.cov
will use 40 threads.