Extracting Split read alignments

Question

[prameelaawale]

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.

[Pierre Lindenbaum]

does the directory 'scripts' exists in the current directory ? try to use a full path for scripts/extractSplitReads_BwaMem instead of a relative path ?