Bam file is malformed using Reduce Reads
I used BaseRecalibration and generated a bam file using PrintReads correctly along with .bai which was generated automatically.
However, when I am trying to reduce the bam file using ReduceReads, I am getting the error below:
ERROR MESSAGE: SAM/BAM file
/bam_base_recalib/dedup_51769_R1_R2_RG_realigned_recal_reads.bam is malformed: Premature EOF; BinaryCodec in readmode; file: /bam_base_recalib/dedup_51769_R1_R2_RG_realigned_recal_reads.bam