SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Base Quality values in BAM file donniemarco Bioinformatics 2 06-22-2011 10:06 AM
.SAM to .BAM with SAM file header @PG emilyjia2000 Bioinformatics 13 06-14-2011 12:21 PM
Single stranded coverage from sam/bam ewilbanks Bioinformatics 2 05-13-2011 11:13 PM
Base coverage from Bam ElMichael Bioinformatics 4 12-01-2010 09:18 AM
Extracting base coverage and quality values from BAM files unagaswamy Bioinformatics 9 11-11-2010 06:55 AM

Reply
 
Thread Tools
Old 02-10-2011, 07:15 PM   #1
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 82
Question 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
ewilbanks is offline   Reply With Quote
Old 02-10-2011, 08:42 PM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

"samtools pileup"
nilshomer is offline   Reply With Quote
Old 02-10-2011, 11:07 PM   #3
Yilong Li
Member
 
Location: WTSI

Join Date: Dec 2010
Posts: 41
Default

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!
Yilong Li is offline   Reply With Quote
Old 02-10-2011, 11:32 PM   #4
droog_22
Member
 
Location: Vienna

Join Date: Nov 2010
Posts: 10
Default

Hi,

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

Cheers
droog_22 is offline   Reply With Quote
Old 02-11-2011, 12:58 AM   #5
boetsie
Senior Member
 
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
Default

Hi lizzy,

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

Hope this helps,
Boetsie
boetsie is offline   Reply With Quote
Old 02-14-2011, 02:14 PM   #6
ewilbanks
Member
 
Location: Davis, CA

Join Date: Mar 2009
Posts: 82
Default

Thanks everyone! I knew you'd all have great suggestions
ewilbanks is offline   Reply With Quote
Old 06-06-2012, 10:40 AM   #7
sagarutturkar
Member
 
Location: Tennessee, USA

Join Date: Sep 2010
Posts: 61
Default

Thanks for the great suggestions. I find it very useful.
sagarutturkar is offline   Reply With Quote
Old 06-06-2012, 01:03 PM   #8
aggp11
Member
 
Location: Wisconsin

Join Date: Jun 2011
Posts: 87
Default

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.
aggp11 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO