bpipe_targeted-enrichment_mouse.config

//file to contain pipeline configuration of MOUSE pipeline


// VARIANT FILTER SCRIPT
FILTER="filter_mouse.sh"

// KNOWN SEQUENCES
REF="${NGS}/refgenome/mm10/mm10_reordered.fa"
CANDIDATES="${NGS}/known_sites/mouse_wes_candidates.txt"

// TARGET SEQUENCES FOR COVERAGE CALC
MOUSE="${NGS}/known_sites/mm10/mouse_wes_padded_mm9lifted2mm10_galaxy_sorted.bed"
TARGET_REGION=MOUSE