<commit_before># TCAG-WGS-CNV-workflow
This repository contains scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods.

If you use any of these scripts, please cite:

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. A comprehensive workflow for read depth-based identification of copy-number variation from whole-genome sequence data. American Journal of Human Genetics 102(1):142-155, 2018.

The workflow in the above paper relies on two CNV-detection tools, which can be obtained as follows.
<commit_msg>Added link to NCBI SRA for HuRef and NA12878<commit_after># TCAG-WGS-CNV-workflow
This repository contains scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods.

If you use any of these scripts, please cite:

<NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and <NAME>. A comprehensive workflow for read depth-based identification of copy-number variation from whole-genome sequence data. American Journal of Human Genetics 102(1):142-155, 2018.

The raw HuRef and NA12878 sequencing data used in the paper are available from:

https://www.ncbi.nlm.nih.gov/sra/PRJNA542535

The workflow in the above paper relies on two CNV-detection tools, which can be obtained as follows.

{'fraction_non_alphanumeric': 0.10829817158931083, 'fraction_numerical': 0.030942334739803096, 'mean_word_length': 5.029661016949152, 'pattern_counts': {'":': 0, '<': 35, '<?xml version=': 0, '>': 35, 'https://': 1, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '433602', 'n_tokens_mistral': 452, 'n_tokens_neox': 395, 'n_words': 191}