I am trying to extract the split read alignments with bwa-mem for pair end sequencing. This is my code.
Extract the split-read alignments
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.