I am using GATK 188.8.131.52. I have been following this guide (https://gatk.broadinstitute.org/hc/en-us/articles/360035889471-How-should-I-pre-process-data-from-multiplexed-sequencing-and-multi-library-designs- ) in order to run Mutect on samples with multiple lanes. Is there anything else I need to do beyond this in order to prepare the samples to run with Mutect2? I tried running Mutect but I noticed that all of the calls have zero reference depth (ie. all alternate depth), which doesn't seem right since I ran this on a slightly older version of Mutect and got something different.
Both my tumor and normal samples are multiplexed. I followed the guide and got these read groups now for my tumor sample (and similarly for the normal):
@RG ID:DS-bkm-085-N_L001_RG SM:DS-bkm-085-N_L001 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_L002_RG SM:DS-bkm-085-N_L002 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_L003_RG SM:DS-bkm-085-N_L003 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_L004_RG SM:DS-bkm-085-N_L004 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_L005_RG SM:DS-bkm-085-N_L005 LB:lib_name PL:illumina
@RG ID:DS-bkm-085-N_L007_RG SM:DS-bkm-085-N_L007 LB:lib_name PL:illumina
There was no error from Mutect so I assumed it was fine. Am I doing something wrong?
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