Shell::Align::Cortex Submit Script

cortex.sh

perl /projectnb/mullenl/programs/CORTEX_release_v1.0.5.15/scripts/calling/run_calls.pl \
--first_kmer 31 \
--last_kmer 61 \
--kmer_step 30 \
--fastaq_index index_file \
--auto_cleaning yes \
--bc yes \
--pd no \
--outdir ./cortexresults \
--outvcf cortextrial \
--ploidy 2 \
--stampy_hash 21G6 \
--stampy_bin /projectnb/mullenl/programs/stampy-1.0.17/stampy.py \
--list_ref_fasta file_listing_fasta \
--refbindir /projectnb/mullenl/data/Ancient_Homology/cortex_trial \
--genome_size 134335 \
--qthresh 5 \
--mem_height 17 \
--mem_width 100 \
--vcftools_dir /projectnb/mullenl/programs/vcftools_0.1.9/ \
--do_union yes \
--ref CoordinatesAndInCalling \
--workflow independent \
--logfile logfile log.txt \
--apply_pop_classifier