├── .gitignore ├── .pytest_cache └── v │ └── cache │ ├── lastfailed │ └── nodeids ├── Files ├── XYlogo.png └── masks │ ├── CNVs │ ├── 1kGchr19_24samples_CNV.vcf │ ├── 1kGchrX_24samples_CNV.vcf │ ├── 1kGchrY_24samples_CNV.vcf │ └── SudmantchrXY19SV_24samples.vcf │ ├── DGV │ ├── DGV_XY19all_mergedGRCh38.bed │ ├── DGV_XY19goldstd_mergedGRCh37.bed │ └── DGV_XY19goldstd_mergedGRCh38.bed │ ├── PARs │ ├── GRCh37_PAR_Ymask.bed │ ├── GRCh37_PAR_Ymask_startEnd.bed │ ├── GRCh38_PAR_Ymask.bed │ ├── GRCh38_PAR_Ymask_startEnd.bed │ ├── README_PARs.txt │ ├── hg19_PAR_Ymask.bed │ ├── hg19_PAR_Ymask_startEnd.bed │ ├── hg38_PAR_Ymask.bed │ └── hg38_PAR_Ymask_startEnd.bed │ ├── Poznik_Y_callable │ ├── Poznik_etal_chrY.callable.hg19.bed.txt │ └── Poznik_etal_chrY.callable.hg38liftover.bed.txt │ ├── gaps │ └── GRCh38.UCSC.gaps.sorted.bed │ ├── lastz_masking_tools │ ├── generate_reference_genome_masks_pipeline.sh │ └── scripts │ │ ├── dotplot.R │ │ ├── dotplot_overlap.R │ │ ├── format_rdotplot.sh │ │ ├── generate_masks.py │ │ └── readme │ └── ucsc_hg38 │ ├── chr10_toMaskRegions_sorted.bed │ ├── chr11_toMaskRegions_sorted.bed │ ├── chr12_toMaskRegions_sorted.bed │ ├── chr13_toMaskRegions_sorted.bed │ ├── chr14_toMaskRegions_sorted.bed │ ├── chr15_toMaskRegions_sorted.bed │ ├── chr16_toMaskRegions_sorted.bed │ ├── chr17_toMaskRegions_sorted.bed │ ├── chr18_toMaskRegions_sorted.bed │ ├── chr19_toMaskRegions_sorted_merged.bed │ ├── chr1_toMaskRegions_sorted.bed │ ├── chr20_toMaskRegions_sorted.bed │ ├── chr21_toMaskRegions_sorted.bed │ ├── chr22_toMaskRegions_sorted.bed │ ├── chr2_toMaskRegions_sorted.bed │ ├── chr3_toMaskRegions_sorted.bed │ ├── chr4_toMaskRegions_sorted.bed │ ├── chr5_toMaskRegions_sorted.bed │ ├── chr6_toMaskRegions_sorted.bed │ ├── chr7_toMaskRegions_sorted.bed │ ├── chr8_toMaskRegions_sorted.bed │ ├── chr9_toMaskRegions_sorted.bed │ ├── chrX_toMaskRegions_sorted_merged.bed │ └── chrY_toMaskRegions_sorted_merged.bed ├── LICENSE ├── README.md ├── analyses ├── README.md └── Webster_etal_2018 │ ├── .gitignore │ ├── README.md │ ├── Snakefile │ ├── Webster_etal_2018_xyalign.config.json │ ├── fastqs │ └── .gitignore │ ├── misc │ ├── .gitignore │ ├── 1000genomes_GRCh38_HighCoverage_ftp_samples.txt │ ├── 1000genomes_metadata.txt │ ├── Get_gene_status.py │ ├── Glossary │ ├── hg19_PAR_Ymask_startEnd.bed │ ├── hg19_Y_region_bed_files │ │ ├── hg19_chrY_ampliconic.bed │ │ ├── hg19_chrY_features_Poznik.bed │ │ ├── hg19_chrY_heterochromatic.bed │ │ ├── hg19_chrY_other.bed │ │ ├── hg19_chrY_par.bed │ │ ├── hg19_chrY_xdegen.bed │ │ └── hg19_chrY_xtrans.bed │ ├── hg19_ccds_genes_chrx.bed │ ├── hg19_chrx_gene_status.txt │ ├── hg19_x_regions.bed │ ├── highCoverage1000genomes_forDownload.txt │ └── seq_comparison_metadata.txt │ ├── processed_bams │ └── .gitignore │ ├── reference │ └── .gitignore │ ├── scripts │ ├── .gitignore │ ├── Plot_read_balance_by_chrY_region.py │ └── Plot_read_balance_with_fixed_overall.py │ ├── snakemake_environment.yml │ ├── xyalign_analyses │ └── .gitignore │ └── xyalign_environment.yml ├── docs ├── .gitignore ├── Makefile ├── api.inc ├── api.rst ├── api │ ├── modules.rst │ ├── xyalign.assemble.rst │ ├── xyalign.bam.rst │ ├── xyalign.ploidy.rst │ ├── xyalign.reftools.rst │ ├── xyalign.rst │ ├── xyalign.utils.rst │ ├── xyalign.variants.rst │ └── xyalign.xyalign.rst ├── conf.py ├── faqs.rst ├── index.rst ├── installation.rst ├── make.bat ├── readthedocs-pip-requirements.txt ├── release.rst └── usage.rst ├── setup.cfg ├── setup.py ├── xyalign ├── .gitignore ├── CHANGELOG.txt ├── __init__.py ├── __main__.py ├── _version.py ├── assemble.py ├── bam.py ├── ploidy.py ├── reftools.py ├── scripts │ ├── .gitignore │ ├── __init__.py │ ├── compare_vcfs.py │ ├── explore_thresholds.py │ ├── plot_count_stats.py │ └── plot_window_differences.py ├── test │ ├── __init__.py │ ├── chr19_window.bam │ ├── chr19_window.bam.bai │ ├── chrX_window1.bam │ ├── chrX_window1.bam.bai │ ├── chrX_window2.bam │ ├── chrX_window2.bam.bai │ ├── dataframe.csv │ ├── fetch.bed │ ├── header.bam │ ├── header.bam.bai │ ├── header2.bam │ ├── hg19_header.bam │ ├── hg19_header.bam.bai │ ├── out.bed │ ├── platypus.bed │ ├── platypus.vcf │ ├── test_assemble.py │ ├── test_bam.py │ ├── test_ploidy.py │ ├── test_reftools.py │ ├── test_utils.py │ ├── test_variants.py │ ├── test_xyalign.py │ ├── tinyheader.bam │ ├── tinyheader.bam.bai │ ├── tinyheader2.bai │ ├── tinyheader2.bam │ ├── toy.bam │ ├── toy.bam.bai │ ├── toy.dict │ ├── toy.fasta │ ├── toy.fasta.amb │ ├── toy.fasta.ann │ ├── toy.fasta.bwt │ ├── toy.fasta.fai │ ├── toy.fasta.pac │ ├── toy.fasta.sa │ ├── toy2.fasta │ ├── toy3.fasta │ ├── toy3.fasta.fai │ ├── toy_1.fastq │ ├── toy_mask.bed │ └── toy_mask2.bed ├── utils.py ├── variants.py └── xyalign.py └── xyalign_runner.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/WilsonSayresLab/XYalign/HEAD/.gitignore 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