I am trying to calculate depth by region using samtools depth command to extract depth information for specific region in chromosome_3 in a bam file.bam
I indexed the bam file using samtools index bamfile.bam to bamfile.bam.bai
when I typed samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai
it gave erorr : could not open "bamfile.bam.bai" : Success
how it could not open the bam.bai file and count it as success?
any help would be highly apprciated
•
written
by
onemore100iq •
samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai
You should point samtools to the bam file, not the index file.
Correctly said by Chris, Input requirement for samtools depth is .bam file not .bai (indexed) file
samtools depth -r <chr:from-to> .bam
Above command should work. (Also make sure that .bam and .bai are in the same directory)
Thanks i did as u said and it worked. Thank u so much
Thanks Chris, it worked. La
Log in to answer this question.
Was this bam files sorted before it was indexed?
yes. and it worked now thanks
You could have a look at https://github.com/brentp/mosdepth