'bamm filter' command with tpmean mode can't produce index file (bai file).

[heavennew]

I used 'bamm make' command to produce a bam and a bai files. But when you used bamm filter command with tpmean mode, no index file (bai file) produced.

How can I fix the problem?

[wwood]

Hi, You can generate bai files with samtools index, but you instead you might try using CoverM https://github.com/wwood/CoverM

Then there is less faffing around - you can just ask for trimmed_mean coverage while at the same time setting read alignment filters.

Hope that helps. ben

[heavennew]

Thank you for your help.