> > Given a BAM file e.g. x.bam the application is looking for the file > x.bam.bai in the same directory. It sounds this is the case? If you create > the index file with samtools : > samtools index x.bam > then it will create x.bam.bai. You could try re-creating the index with > samtools. >
I think the .bam file needs to be SORTED too (by reference coordinates) before indexing. Chances are it already is sorted (as it was used with USCS) but just in case: % samtools sort original.bam original-sorted # will create original-sorted.bam % samtools index original-sorted.bam NOTE that for the sort command, you don't put the .bam suffix ... it does it itself (ech). -- --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA
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