[Samtools-help] bam index file name

[Rusch, M. <Mic...@ST...>]

When I index a bam using samtools, it appends .bai to the filename like this:

input.bam
input.bam.bai

When I used Picard, it replaces bam with bai:

input.bam
input.bai

>From what I can see, Picard is able to recognize an index using the .bam.bai extension, but samtools is not able to find the index with the plain .bai extension.

>From what I see, the .bam.bai convention is universally recognized.  Is that true?

Is there a reason for the two different conventions?

I'd like to move to generating the index file as part of MarkDuplicates since it saves a step.  Since .bam.bai seems to be more widely accepted, my plan at the moment is to wrap in a script that will rename the .bai file after MarkDuplicates is done.  Is there a better way?

Michael

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