December 16, 2015 at 9:26 am #1825
Dear novocraft developers
I have a number of aligned files from the same library and run. They do not contain any read group information. I would like to combine (merge) them, add RG info, mark duplicates and in the end sort by coordinate. Can all this be done using novosort in one step? E.g. novosort in1.bam in2.bam
-o out.bam -i –rg “@RG\tID:X\tLB=X\tPL=X\tPU=X\tSM=X\tCN=LX” –markDuplicates 2>log.txt
If not, can some of these steps be combined?
Thank you beforehand,
Best regardsDecember 16, 2015 at 9:37 am #1826
As long as you are adding the same @RG to all the BAMs then it can be done in one novosort command.
KR, ColinDecember 16, 2015 at 9:38 am #1827
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