Simple question, is it possible to run samtools index (or any of the samtools in fact) on multiple bam files at the same time from the command line? I tried $ samtools index *.bam from within the directory with all more bam files stored and got the following error
Samtools-htslib-API: bam_index_build2() not yet implemented
Abort trap: 6
I also had a go at using $ ls *.bam | samtools index which also didn't work. To note, my bam files are all co-ordinate sorted. I went through the pain of doing that one by one.
It would be especially useful to be able to use samtools on multiple files when it comes to filtering on MAPQ scores etc etc.