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Old 07-20-2011, 05:52 AM   #1
Location: United Kingdom

Join Date: Mar 2011
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Default samtools merge

I know there are many threads on samtools merge command but unfortunately, I am yet to find my answer. I hope someone can help me out in this!
I have just one sample (SOLiD data) with two different libraries - A and B.
A has 3 mate pair reads and 2 fragments. B has 1 paired end read.
I wish to merge all the above bam files into one for snp calling.
I tried it with
samtools merge -r out.bam in1.bam in2.bam in3.bam ...etc

I obtained a out.bam file. Now I tried to call for the snps but when I run the command it gives me an error stating

[group_smpl] Read group <B_sample.hg19> used in file <out.bam> but absent from the header or an alignment missing read group.

I would appreciate any suggestions..

Thank you.

Last edited by nans_bn; 07-20-2011 at 05:55 AM.
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Old 07-21-2011, 08:26 AM   #2
Nils Homer
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Location: Boston, MA, USA

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Try using the merge facility within Picard. It should handle merging headers properly.
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Old 07-22-2011, 04:45 AM   #3
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Great, thanks a lot. I'll try that out.
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