samtools merge

nans_bn · 07-20-2011, 05:52 AM

Hello,
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.

nilshomer · 07-21-2011, 08:26 AM

Try using the merge facility within Picard. It should handle merging headers properly.

nans_bn · 07-22-2011, 04:45 AM

Great, thanks a lot. I'll try that out.

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07-20-2011, 05:52 AM	#1
nans_bn Member Location: United Kingdom Join Date: Mar 2011 Posts: 12	samtools merge Hello, 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.

07-21-2011, 08:26 AM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Try using the merge facility within Picard. It should handle merging headers properly.

07-22-2011, 04:45 AM	#3
nans_bn Member Location: United Kingdom Join Date: Mar 2011 Posts: 12	Great, thanks a lot. I'll try that out.