Convert merged BAM back to per lane BAM or FASTQ file

danielsbrewer · 09-28-2011, 08:40 AM

I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis pipeline. Any ideas on the best way to do this?

gringer · 09-28-2011, 01:49 PM

When I did this a few days ago (with only knowledge of command-line stuff and samtools), here's a rough guide to what I did:

Extract header from BAM file

Code:

samtools view -H infile.bam > header.sam

filter out lanes from BAM file, add header

Code:

(cat header.sam; samtools view infile.bam | grep '^DATA...._<lane>_.') > out_lane<lane>.sam

convert SAM to BAM

Code:

samtools view -S out_lane<lane>.sam -b > out_lane<lane>.bam

There's probably some better way, but it would have taken longer for me to find than for me to just do it and deal with the additional overhead of storing temporary SAM files per lane.

Chipper · 09-28-2011, 02:09 PM

If the lane info is stored in RG tags you can use this: http://genome.sph.umich.edu/wiki/SplitBam

danielsbrewer · 09-29-2011, 01:50 AM

SplitBam looks ideal, but I can't find a download link for it. Any ideas?

And thanks for the other suggestion too, that makes a lot of sense.

--EDIT--
Actually it looks like there are no @RG in the headers ... Oh Dear.

jtladner · 10-06-2011, 06:06 PM

I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

Jason

kmcarr · 10-07-2011, 06:17 AM

Quote:

Originally Posted by danielsbrewer

SplitBam looks ideal, but I can't find a download link for it. Any ideas?

And thanks for the other suggestion too, that makes a lot of sense.

--EDIT--
Actually it looks like there are no @RG in the headers ... Oh Dear.

Quote:

Originally Posted by jtladner

I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

Jason

Go here and either follow the instructions for retrieving the current development release from the source repository or download the tarball for the latest stable realese (0.1.4). Note that either way you are downloading the entire libStatGen toolkit, which you must then compile. SplitBam is merely one of the programs in the toolkit.

zebrafisch · 10-03-2013, 08:29 AM

Quote:

Originally Posted by jtladner

I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program?

Jason

splitBam is part of the bamUtil package, which i found it here https://github.com/Homebrew/homebrew-science and it was very easy to download it.

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09-28-2011, 08:40 AM	#1
danielsbrewer Member Location: UK Join Date: Feb 2009 Posts: 33	Convert merged BAM back to per lane BAM or FASTQ file I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq) so it would be compatible with the analysis pipeline. Any ideas on the best way to do this?

09-28-2011, 01:49 PM	#2
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	When I did this a few days ago (with only knowledge of command-line stuff and samtools), here's a rough guide to what I did: Extract header from BAM file Code: samtools view -H infile.bam > header.sam filter out lanes from BAM file, add header Code: (cat header.sam; samtools view infile.bam \| grep '^DATA...._<lane>_.') > out_lane<lane>.sam convert SAM to BAM Code: samtools view -S out_lane<lane>.sam -b > out_lane<lane>.bam There's probably some better way, but it would have taken longer for me to find than for me to just do it and deal with the additional overhead of storing temporary SAM files per lane.

09-29-2011, 01:50 AM	#4
danielsbrewer Member Location: UK Join Date: Feb 2009 Posts: 33	SplitBam looks ideal, but I can't find a download link for it. Any ideas? And thanks for the other suggestion too, that makes a lot of sense. --EDIT-- Actually it looks like there are no @RG in the headers ... Oh Dear. Last edited by danielsbrewer; 09-29-2011 at 02:03 AM.

10-06-2011, 06:06 PM	#5
jtladner Junior Member Location: California Join Date: Feb 2010 Posts: 3	SplitBam download link? I am trying to do the exact same thing and I do have @RG tags, but I can not find a download link for SplitBam. Does anyone know how to download this program? Jason

09-28-2011, 02:09 PM	#3
Chipper Senior Member Location: Sweden Join Date: Mar 2008 Posts: 324	If the lane info is stored in RG tags you can use this: http://genome.sph.umich.edu/wiki/SplitBam