Any Tools to calculate specific gene coverage from BAM file?

Question

[koay]

Hi all,

I have a BAM file from human whole exome sequencing data. I am looking for a tool (Windows OS) that can calculate the coverage for specific gene output.

For instance, I am using VarAFT Tool. I can look at specific gene, let's say PKD2, and the tool can output coverage 1x (100%), coverage 5x (95.2%), coverage 10x (93.5%), coverage 20x (90.1%) and coverage 30x (82.7%).

I am trying to look for specifically coverage 15x so that I can make comparison with other papers but to no success. If anyone can recommend a tool that can be used on Windows OS and calculate specific gene at coverage 15x, please let me know.

Thank you.

[colindaven]

Please don't try to use Windows OS for bioinformatics, as most tools are not written or tested on windows. If you absolutely must, then either buy commercial software, or better, use Galaxy (requires only a web browser).

[jared.andrews07]

Or just use [the Windows Subsystem for Linux], which works well. There is no longer any real reason to avoid using Windows machines for bioinformatics.

[colindaven]

duplicated

Answer 1

[Pierre Lindenbaum]

mosdepth --by a_bed_for_your_gene.bed --thresholds 1,5,10,15,20,30 OUT in.bam

[koay]

This worked out for me. Thank you.

Answer 2

[wulj2]

look up your gene coordinates from NCBI/UCSC, and use samtools to extract the coverage/depth information form you BAM, do whatever you like from then on...