a simple question

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

a simple, very simple question, for visualization of a specific region in IGV.

I would like to extract a specific region of a BAM file, that works fine with :

samtools view -h file.MD.bam chr7:152118000-152474000 > file.MD.region.bam

now in order to visualize the file "file.MD.region.bam " in IGV, it needs an index.

or the command : "samtools index file.MD.region.bam " does not produce anything ...

please could you advise, what am I doing wrong ? many thanks,

-- bogdan

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