index not found for gatk output
Opened this issue · 1 comments
crazyhottommy commented
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 commented
I do not know any C, unfortunately.