Per base sequence coverage from sam/bam file?

[ewilbanks]

Hi all,

Does anyone have recommendations for good progams for calculating the per base sequence coverage for mapped reads in sam or bam format? I'd like for the output format to be human readable (not tdf) so I can input into R for downstream analysis.

Sorry if this seems basic-- I just haven't been able to lay hands on just the right script and I'm sure there's one out there somewhere that will be faster than something my newbie-self can program!

Thanks!!!
Lizzy

[nilshomer]

"samtools pileup"

[Yilong Li]

I think GATK -T DepthOfCoverage also does the job. I haven't tried the per-base coverage in GATK myself (= ran it with -omitBaseOutput), but I think samtools pileup omits bases with no coverage, so might require additional additional scripting after running the pileup. Please correct me if I'm wrong!

[droog_22]

Hi,

You can use genomeCoverageBed from the http://code.google.com/p/bedtools/ which can also read in BAM files.

Cheers

[boetsie]

Hi lizzy,

see my older thread at http://seqanswers.com/forums/showthread.php?t=7679

Hope this helps,
Boetsie

[ewilbanks]

Thanks everyone! I knew you'd all have great suggestions

[sagarutturkar]

Thanks for the great suggestions. I find it very useful.

[aggp11]

I find "samtools depth" pretty useful. The fact that you can get coverage for a list of target regions and also look for coverage with different base and mapping quality.