how to read indexed bamfiles

Question

[onemore100iq]

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

[GenoMax]

Was this bam files sorted before it was indexed?

[onemore100iq]

yes. and it worked now thanks

[WouterDeCoster]

You could have a look at https://github.com/brentp/mosdepth

Answer 1

[Chris Miller]

samtools depth -r chromosome_3:10001-10010 bamfile.bam.bai

You should point samtools to the bam file, not the index file.

[Samarth Kulshrestha]

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)

[onemore100iq]

Thanks i did as u said and it worked. Thank u so much

[onemore100iq]

Thanks Chris, it worked. La