WGS Structural Variation Pipeline Software Version: python/3.6.1 extract_sv_reads/1.1.2 lumpy-sv/v0.2.13 svtyper/v0.1.4
Computational requirements: hoffman2 4-core 8gb-ram
Run Time: 2-3hr/sample Read Extraction + Lumpy ~10hr/sample svtyper
Example run:
lumpy_submission_shell.sh (edit paths to scratch / list of bams to call (line seperated), all bams should be indexed, calls SGE job array, call lumpy_variant.sh per sample)
sort.py, merge.py part of lumpy package
bnd_remover.py -i input_list -o output_suffix -d directory_path
sv_typer_submission_shell.sh (edit paths to scratch / list of bams to call (line seperated), all bams should be indexed, calls SGE job array, call svtyper_shell.sh per sample)