how do i create an rg.txt file for input into samtools merge? / picard

lexi · 08-29-2013, 10:59 PM

Hi,

I have merged bam files from 6 lanes for a number of samples, and am trying to use picard MarkDuplicates. However, I get an error PicardException: Value was put into PairInfoMap more than once. Which I've learn is due to some issues with the read group information.

I'm planning to rerun samtools merge using the -r and -h options (ie samtools merge -rh rg.txt in1.bam in2.bam in3.bam in4.bam in5.bam in6.bam out.bam) but I'm not sure what file to use for the -h option, what needs to be included etc in the required file. Could anyone please let me know where to get the file format or what information to include?

Thanks in advance

bishwo · 08-30-2013, 12:15 AM

When merging different bam files, reads from those bam files need some way to be distinguished. It can also be done by using AddOrReplaceReadGroups from picard tools (I prefer picard tools to samtools). If you use picard tools read group headers are give in commandline. As far as i remember you need to put them in file if you use Sam tools. RG is described in SAM format specification. YOu can also find read group headers in AddOrReplaceReadGroups page.

dpryan · 08-30-2013, 04:20 AM

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08-29-2013, 10:59 PM	#1
lexi Junior Member Location: Australia Join Date: Jul 2013 Posts: 1	how do i create an rg.txt file for input into samtools merge? / picard Hi, I have merged bam files from 6 lanes for a number of samples, and am trying to use picard MarkDuplicates. However, I get an error PicardException: Value was put into PairInfoMap more than once. Which I've learn is due to some issues with the read group information. I'm planning to rerun samtools merge using the -r and -h options (ie samtools merge -rh rg.txt in1.bam in2.bam in3.bam in4.bam in5.bam in6.bam out.bam) but I'm not sure what file to use for the -h option, what needs to be included etc in the required file. Could anyone please let me know where to get the file format or what information to include? Thanks in advance

08-30-2013, 12:15 AM	#2
bishwo Junior Member Location: Finland Join Date: Jan 2012 Posts: 8	When merging different bam files, reads from those bam files need some way to be distinguished. It can also be done by using AddOrReplaceReadGroups from picard tools (I prefer picard tools to samtools). If you use picard tools read group headers are give in commandline. As far as i remember you need to put them in file if you use Sam tools. RG is described in SAM format specification. YOu can also find read group headers in AddOrReplaceReadGroups page. Last edited by bishwo; 08-30-2013 at 12:19 AM.

08-30-2013, 04:20 AM	#3
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	See also the same question on biostars.