I have 152 coordinate sorted bam files. I want to merge them. I have tried both Samtools merge and Picard. I used Samtools merge before on some different data and it worked but I don't think that data was coordinate sorted and that might make a difference. The command I am trying to use is
samtools merge /out.bam /path_to_file/*.bam
I want it to merge all the files in that folder. I don't get a specific error but it prints out the samtools merge usage parameters. So I guess I am missing something in my command. The following is what I have done so far in my pipeline:
1. aligned with bowtie 2 (output sam)
2. sorted individual sam files output to individual bam files
The end goal is to use GATK for variant analysis. According to http://seqanswers.com/wiki/How-to/exome_analysis, I need to put some kind of -r argument in Samtools when I am processing to add an @rq (or something like that).
I am lost at this moment and I have searched and searched to try and find an answer on the forums.
samtools merge /out.bam /path_to_file/*.bam
I want it to merge all the files in that folder. I don't get a specific error but it prints out the samtools merge usage parameters. So I guess I am missing something in my command. The following is what I have done so far in my pipeline:
1. aligned with bowtie 2 (output sam)
2. sorted individual sam files output to individual bam files
The end goal is to use GATK for variant analysis. According to http://seqanswers.com/wiki/How-to/exome_analysis, I need to put some kind of -r argument in Samtools when I am processing to add an @rq (or something like that).
I am lost at this moment and I have searched and searched to try and find an answer on the forums.
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