Read more about it here!
Question concerning BaseRecalibrator
To whom it may concern,
after running the realignment and creating a corresponding xxx_realigned.bam, I tried to recalibrate bases using walker BaseRecalibrator. The walker stopped analysis due to the ERROR MESSAGE: SAM/BAM file xxx_realigned.bam is malformed: Read error; BinaryCodec in readmode; file: /....
As I can't figure out the problem, I hope to get some help.