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picard pacbio

I have done the Pacio reads alignment with BWA-SW,and generate a .sam file,how can I tranfer the .sam to .bam with header?
I used samtools and picard ,but I could not gain a .bam with header.What the Addorreplacereadgroups parameter RGID,RGLB,RGPL,RGPU,RGSM should be with Pacbio data??


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    With Picard tools, you just need to specify the output file name with ".bam" as suffix, and the tool will automatically write a bam file instead of a Sam file.

    Regarding the read group information, please look up the sam/bam file specification to learn what these fields describe.

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