<commit_before>example of a snakemake dedicated to variant calling.

TODO:

Refine freebayes params

VCF filter.

SNPeff
<commit_msg>Add information about the pipeline.<commit_after>Example of a snakemake dedicated to variant calling.
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This pipeline does the variant calling of a bam file. The first rule is markDuplicate. It is an optional rule. You must indicate in the config file if you wish to activate this rule. (true/false)

The second rule indexes your bam file. And finally, the last rule call freebayes to detect snp and indel variants.

TODO:
-------
- Mapping rule ?

- Refine freebayes params

- VCF filter.

- SNPeff

{'fraction_non_alphanumeric': 0.1282798833819242, 'fraction_numerical': 0.0, 'mean_word_length': 4.204545454545454, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, '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': '7562913', 'n_tokens_mistral': 195, 'n_tokens_neox': 186, 'n_words': 91}