index not found for gatk output

[crazyhottommy]

Hi,

If the index is created by samtools, the name of the index is sample.sorted.bam.bai
if it is created by gatk, it is sample.sorted.bai.

bam-readcount complains for the gatk bai file

Minimum mapping quality is set to 0
Expect library: Pa25T2-T in BAM
[bam_index_load] fail to load BAM index.
BAM indexing file is not available.

it should be a quick fix.

Thank you,

Tommy

[crazyhottommy]

I do not know any C, unfortunately.