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Retrieve base count information for bases that are not variants

I am analysing RNA-seq data and I require read/allele depth information for a particular base position (I need this information for about 50 positions scattered around the genome in 8 individuals). As variant callers only give read depth information for variants, most of the positions I need are not SNV's in many of my samples (they are reference homozygotes) and so will not be called by variant callers. VCF files give the information I need but only for variants. Does anybody know a way I can get this information quickly? I really do not want to go into IGV and manually look for allele depth for by 50 bases in all 8 samples. Any help will be very appreciated. Thanks

rna-seq base read depth
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by rjobmc • rjobmc

1 answer 

samtools depth f1.bam f2.bam f3.bam
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written by Pierre Lindenbaum Pierre Lindenbaum

Will this provide a read depth for every base in my bam file?

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written by rjobmc • rjobmc

Yes it can.

-a                  output all positions (including zero depth)
-a -a (or -aa)      output absolutely all positions, including unused ref. sequences

Use mosdepth ( https://github.com/brentp/mosdepth ) for faster turnaround.

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written by GenoMax GenoMax

In the end I used samtool depth a1.bed f1.bam, f2.ba etc.... a1.bed is a bed file with my positions. This worked perfectly! Thank you very much for your help.

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written by rjobmc • rjobmc

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