MuTect Bam input files

[himanshu04]

Dear Community,
I am trying to run MuTect on my RNA seq samples aligned by Tophat.
I get the error that my bam files are not indexed. I have sorted them, marked duplicates, Added group headers and indexed them both (tumor and normal).

What am I doing wrong?. Can anyone help me?.
Thanks,
Himanshu

[lethalfang]

Dear Community,
I am trying to run MuTect on my RNA seq samples aligned by Tophat.
I get the error that my bam files are not indexed. I have sorted them, marked duplicates, Added group headers and indexed them both (tumor and normal).

What am I doing wrong?. Can anyone help me?.
Thanks,
Himanshu

Different people have difference experiences with Broad's stuff.
For me, merging/sorting/indexing by samtools didn't work with MuTect, but doing the same things with picard worked.
If you merged, sorted, and indexed with samtools, try with picard.