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I ran BaseRecalibrator on some of my realigned bam files, there were no errors reported while running it and I was to able to generate the "recal.grp" files. However, while running the PrintReads walker to generate the recalibrated BAM files, I get the following error message for some of the BAMs.
##### ERROR MESSAGE: Exception when processing alignment for BAM index WTCHG_35305_101:4:1105:10332:129428#TGTTAACT 2/2 100b aligned read.
So, I tried to validate my realigned BAM as well as the original BAM before realignment using Picard's ValidateSAMFile and I get the following:
original BAM: Mate unmapped flag does not match read unmapped flag of mate, Mate alignment does not match alignment start of mate, Mate negative strand flag does not match read negative strand flag of mate
Aditionally these errors on realigned BAMs: Mate reference index (MRNM) does not match reference index of mate, Mate not found for paired read
Do I need to worry about initial alignments? I read on the forums that using -rf MateSameStrand Filter should help me work around this, what does this filter exactly do? Any other approaches to solve this problem would be appreciated.