Hello all:
If I were to use GATK's local realigner outside of GATK pipeline, eg:
BWA -> GATK's Local Realigner -> SAMTools
then will I have any extra problems because I use non-GATK modules upstream or downstream of realignment?
Thanks,
Nik
If I were to use GATK's local realigner outside of GATK pipeline, eg:
BWA -> GATK's Local Realigner -> SAMTools
then will I have any extra problems because I use non-GATK modules upstream or downstream of realignment?
Thanks,
Nik
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