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###This is a readme file that list what all the scripts do and in what order they should be used #aligning reads #align with bwa #generate sam/bam files. index files with samtools #filter out bad reads and do local realignments with gatk. bwa.R #calling snps with samtools mpileup samtools_mpileup.R #cleaning up and parsing the snps. samtools_mpileup_aftermpileup.R snp_parser.R #are the non-synynomus snps deleterious. there are 2 alternative versions (d and w) depending on the reference (domesticated only or wild only) #See methods in the paper for more info. but essentially, you should not use dprovean.R and wprovean.R, they might not be up-to-date. provean_sift.R # this also runs SIFT dprovean.R wprovean.R #parsing the provean/sift results provean_afterprovean.R provean)aftersift.R #are snps syn. non-syn. non-coding? syn_nonsyn_vII.R #calculate nucleotide diversity using SITES from Jody Hey's lab pi.R #redo figure 1, but with different missing data thresholds. missingdata_check_alignments_fractions.R #find out the effect of recombination rate recomrate.R #plotting all the Figures, unless a figure is specified in another script plotting.R #generate table S1 and some other alignment stats... table_S1.R