Bam2Seq

This tool takes a BAM file containing CIGAR strings, reads, and MD tags, and outputs a .seq file containing pairs of reads and reconstructed references.

Installation

Install directly with cargo from crates.io:

cargo install bam2seq

Simply clone the repository, and optionally install the binary.

git clone https://github.com/ragnargrootkoerkamp/bam2seq.git
cd bam2seq
cargo install --path .

Usage

cargo run --release -- <input.bam> [<output.seq>] [--no-clip] [--min-len <len>]

input.bam

The input BAM file.

output.seq

The output .seq file. Defaults to input.seq.

--no-clip

Disable trimming of soft clipped regions from the read.

--min-len <len>

Only output (clipped) reads of at least this length.

This outputs a .seq file, which looks like this:

>ACTGATGA
<ACAGATG
>read 2
<reference 2
...

Links

• This is quite similar to sam2pairwise but writes a simpler output format.
• All the work in the implementation is done by the BAM crate.