├── .gitignore ├── Ensembl.dat-to-topGO.db.py ├── FastaToPhylip.py ├── FastaToTab.py ├── GFFextract.py ├── LICENSE ├── MAF-Calls_alignment-complement.py ├── MAF-TAB_reference.py ├── MAFtoTAB.py ├── README.md ├── RefSeqGene_extract_summary.py ├── addGOannotation-to-gff3.py ├── add_noise_to_0.py ├── annotate_genes_withSlidingWindowsStats.py ├── assessNs_in_callsTab.py ├── beagleVCF_to_calls.py ├── calculateNsPerWindow.py ├── calls.py ├── callsToBED.py ├── callsToFastaPhy_RAM.py ├── callsToFastaPhy_speed.py ├── calls_to_XPCLR_input.py ├── calls_to_fastPHASE.py ├── calls_to_ped_map.py ├── calls_to_treeMix_input.py ├── collapse_overlapping_intervals.py ├── combine_overlapping_BEDintervals.py ├── extractSIFT4Gannotation.py ├── filterByNs_callsTab.py ├── findCommonAlleles.py ├── find_popSpecificAlleles_in_callsTab.py ├── keep_biallelic_in_callsTab.py ├── makeSweepFinderInput_from_callsTab.py ├── make_custom_map.py ├── make_input_MSMC_from_callsTab.py ├── make_input_stairway_plot_v1_BS.py ├── make_input_stairway_plot_v2.py ├── mergeChrPos_in_callsTab.py ├── mergeTabFiles.py ├── merge_CNVs_tabs.py ├── merge_SNP_wholeGenome_TabFiles.py ├── merge_intervals_phastCons.py ├── merge_overlaping_windows_replaceOverlap.py ├── merge_phased_callsTab.py ├── merge_windowScores_SNPs.py ├── numberSNPsPerWindows.py ├── polarizeGT_in_callsTab_keepDerived.py ├── polarize_beagleVCF.py ├── polarize_callsTab.py ├── pseudoPhasingHetero_in_callsTab.py ├── removeMonomorphic_in_callsTab.py ├── remove_Insertions_from_callsTab.py ├── remove_masked_intervals_fromBED.py ├── remove_masked_intervals_from_callsTab.py ├── selectSamples_in_callsTab.py ├── select_genes_by_intervals.py ├── select_interval_info_for_genotypes.py ├── select_intervals_in_callsTab.py ├── slidingWindowSNPs.py ├── snp_annotation_to_genes_annotation.py ├── split_calls_by_chromosomes.py ├── summarizeTAB.awk ├── summarySIFT.awk ├── vcfTab_to_callsTab.py └── vcf_to_SIFT4G.py /.gitignore: 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