CNVKIT_IMPORT-PICARD(1)

CNVKIT_IMPORT-PICARD 💅✨

okay bestie, welcome to the User Commands section of the manual, section 1, and this is literally the glow-up guide for cnvkit_import-picard. buckle up 🎀

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🌸 NAME 🌸

cnvkit_import-picard — the lil icon that converts Picard CalculateHsMetrics tabular output into CNVkit .cnn files. no cap. 🦋

so here's the tea: the input file gets generated by the PER_TARGET_COVERAGE option in the CalculateHsMetrics script in Picard tools. that's the whole source of the drama. 👑

and lowkey the most important part — the filename sleuthing: if 'antitarget' is in the input filename, the generated output filename will have the suffix .antitargetcoverage.cnn, otherwise it'll have .targetcoverage.cnn. the filename decides its own fate, main character energy fr fr. ✨

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💖 DESCRIPTION 💖

the usage line, exactly as it lives:

usage: cnvkit.py import-picard [-h] [-d DIRECTORY] targets [targets ...]

🎀 positional arguments: 🎀

• targets — the sample coverage .csv files, both target and antitarget ones. feed me the whole set, bestie. 🍓

✨ options: ✨

• -h, --help — shows this help message and then dips. exit stage left. 💅
• -d DIRECTORY, --output-dir DIRECTORY — the output directory name. that's where your freshly converted files go to live their best life. 🫶

ngl there are only two options here, and honestly? iconic of it to be so unbothered. 😌

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and that's the whole page, bestie!! written by cnvkit.py import-picard version 0.9.10, dated July 2023, and yeah — CNVKIT_IMPORT-PICARD(1) really said "short, sweet, slay" and left. go convert some coverage files, you absolute legend 👑💖✨