Per base sequence coverage from sam/bam file?

ewilbanks · 02-10-2011, 08:15 PM

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 · 02-10-2011, 09:42 PM

"samtools pileup"

Yilong Li · 02-11-2011, 12:07 AM

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 · 02-11-2011, 12:32 AM

Hi,

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

Cheers

boetsie · 02-11-2011, 01:58 AM

Hi lizzy,

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

Hope this helps,
Boetsie

ewilbanks · 02-14-2011, 03:14 PM

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

sagarutturkar · 06-06-2012, 11:40 AM

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

aggp11 · 06-06-2012, 02:03 PM

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.

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02-10-2011, 08:15 PM	#1
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	Per base sequence coverage from sam/bam file? 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

02-10-2011, 09:42 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	"samtools pileup"

02-11-2011, 12:07 AM	#3
Yilong Li Member Location: WTSI Join Date: Dec 2010 Posts: 41	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!

02-11-2011, 12:32 AM	#4
droog_22 Member Location: Vienna Join Date: Nov 2010 Posts: 10	Hi, You can use genomeCoverageBed from the http://code.google.com/p/bedtools/ which can also read in BAM files. Cheers

02-11-2011, 01:58 AM	#5
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	Hi lizzy, see my older thread at http://seqanswers.com/forums/showthread.php?t=7679 Hope this helps, Boetsie

02-14-2011, 03:14 PM	#6
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	Thanks everyone! I knew you'd all have great suggestions

06-06-2012, 11:40 AM	#7
sagarutturkar Member Location: Tennessee, USA Join Date: Sep 2010 Posts: 61	Thanks for the great suggestions. I find it very useful.

06-06-2012, 02:03 PM	#8
aggp11 Member Location: Wisconsin Join Date: Jun 2011 Posts: 87	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.