├── .gitignore ├── GenomeAnalysisTK ├── LICENSE.txt ├── MarkDuplicates ├── PicardMerge ├── README.markdown ├── SortSam ├── count_flagstat_wgs.py ├── example_data ├── input_data_wgs │ ├── NA12878wgs_20FUKAAXX_NA_L006_R1.fastq.gz │ ├── NA12878wgs_20FUKAAXX_NA_L006_R2.fastq.gz │ ├── NA12878wgs_20FUKAAXX_NA_L007_R1.fastq.gz │ ├── NA12878wgs_20FUKAAXX_NA_L007_R2.fastq.gz │ ├── NA12878wgs_20GAVAAXX_NA_L006_R1.fastq.gz │ ├── NA12878wgs_20GAVAAXX_NA_L006_R2.fastq.gz │ ├── NA12878wgs_20GAVAAXX_NA_L007_R1.fastq.gz │ ├── NA12878wgs_20GAVAAXX_NA_L007_R2.fastq.gz │ └── README └── output_wgs │ ├── README │ └── fastq_symlinks │ └── README ├── input_fastq.py ├── pipeline.py ├── pipeline_dev_config.py ├── pipeline_stages_config.py └── vcftools_prepare.sh /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /GenomeAnalysisTK: 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