This pipeline maps, decontaminates and calls variants for pooled drosophila melanogaster sequence data.
##00_reference Download D. melanogaster and D. simulans reference genomes
##01_sample_data Create symlinks (to save diskspace) to all raw sequence data. Also, split 2012-nescent data by barcode and trim barcodes.
##02_mapping Map raw reads to reference genome using bwa-mem, deduplicate, re-align using GATK. (plus fix phred scores for some read libraries).
##03_divergence Identify SNPs that are 100% divergent between Drosophila melanogaster and Drosophila simulans. These divergent SNPs can be used to test for D. simulans contamination in the D. melanogaster pooled sequences.
##04_detect_contamination Test for D. simulans contamination in the D. melanogaster pooled samples.
##05_decontaminate Decontaminate the contaminated samples by competitive mapping to D. melanogaster and D. simulans genomes.
##06_call_variants Use CRISP to call variants.
##07_process_VCF Fix some errors in CRISP output, convert allele frequenceis to ad:dp format, deal with multiple allele SNP per row (unwind so that 1 allele per row), calculate distance to nearest indel, format VCF for import into a SQL type database.