I am trying to extract the split read alignments with bwa-mem for pair end sequencing. This is my code.
samtools view -h rscm2.bam | scripts/extractSplitReads_BwaMem -i stdin | samtools view -Sb - > rscm2.splitters.unsorted.bam
But I am getting this error message.
/cm/local/apps/slurm/var/spool/job16557014/slurm_script: line 18: scripts/extractSplitReads_BwaMem: No such file or directory
Can anyone please help to fix this error?
Thank you in advance.