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

    Leave a comment:


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

    Leave a comment:


  • nans_bn
    started a topic samtools merge

    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, 04:55 AM.

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