hi all,
A seemingly simple task of merging BAMs has flummoxed me. Picard MergeBamAlignment module has a mandatory option of UNAMAPPED_BAM file.
I am using bwa aln and it doesn't return separately any unmapped file. I couldn't understand this parameter. Is this module supposed to be used only if one has unmapped BAMs too.
Anyways, another Picard module: MergeSamFiles, says it can merge BAMs too and doesn't require unmapped BAMs.
I spent so much time understanding the former; thought anyone else looking at these modules should be aware too.
A seemingly simple task of merging BAMs has flummoxed me. Picard MergeBamAlignment module has a mandatory option of UNAMAPPED_BAM file.
I am using bwa aln and it doesn't return separately any unmapped file. I couldn't understand this parameter. Is this module supposed to be used only if one has unmapped BAMs too.
Anyways, another Picard module: MergeSamFiles, says it can merge BAMs too and doesn't require unmapped BAMs.
I spent so much time understanding the former; thought anyone else looking at these modules should be aware too.
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