AddOrReplaceReadGroups read only specific chromosomes

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2.9 years ago

adrian18_07 ▴ 10

I have a BAM file where there are readings for different chromosomes. I would like to use the AddOrReplaceReadGroups function for chr1 and chr2 only. Can this be defined in a function? Do I have to use e.g. samtools to extract the chromosomes first?

BAM GATK4 AddOrReplaceReadGroups • 539 views

ADD COMMENT • link updated 2.9 years ago by Pierre Lindenbaum 164k • written 2.9 years ago by adrian18_07 ▴ 10

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Entering edit mode

I would like to use the AddOrReplaceReadGroups function for chr1 and chr2 only.

just curious: why ?

ADD REPLY • link 2.9 years ago by Pierre Lindenbaum 164k

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