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 or what to include?
Thanks in advance