Description

bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

reference (file)

Reference genome FASTA file

*.{fa,fasta,fa.gz,fasta.gz}

bed (file)

BED file with regions to analyze

*.bed

Output

Name
Description
Pattern

0 ()

0 ()

Tools

bamreadcount Documentation

bam-readcount generates metrics at single nucleotide positions.

https://github.com/genome/bam-readcountdoi: 10.21105/joss.03722License: MIT
Authors