├── .gitignore ├── .gitmodules ├── LICENSE.md ├── README.md ├── align_check.sh ├── align_check_template.sh ├── align_template.sh ├── concatenate ├── cat_align.sh ├── cat_muse.sh ├── cat_mutect.sh ├── cat_pon.sh ├── cat_postalign.sh ├── cat_strelka.sh └── cat_varscan.sh ├── gatk3_env.yml ├── main_env.yml ├── muse_template.sh ├── mutect_template.sh ├── pon_template.sh ├── refine_check.sh ├── refine_check_template.sh ├── refine_template.sh ├── run_evc.sh ├── run_evc_bam.sh ├── run_evc_precancer.sh ├── setup_MuSE.sh ├── setup_env.sh ├── start_align.sh ├── strelka_env.yml ├── strelka_template.sh ├── targetInterval_template.sh └── varscan_template.sh /.gitignore: -------------------------------------------------------------------------------- 1 | MuSE/ 2 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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