SMOOTHER(1)

💖 SMOOTHER — the NAME bit 💖

okay so the command is smoother and it lives in the smoother manual, filed under VCF transformation. that's the whole vibe check for the name section bestie ✨

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🌸 SYNOPSIS 🌸

smoother –format pFst –file GPA.output.txt

that's it. that's the whole summoning ritual 💅

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🦋 DESCRIPTION 🦋

so smoothes is a method for window smoothing, and it works on a whole bunch of the GPAT++ formats. that's literally the entire description. short queen, no filler 👑

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✨ OPTIONS ✨

okay this is the part where the girlies get lost so let me hold your hand through it 🫶

smoother averages a set of scores over a sliding genomic window.

smoother slides over genomic positions, not the SNP indices. translation: the number of scores inside a window will not be constant, so don't come for me when the count is different every time 😭 and heads up — the last window for each seqid can be smaller than the defined window size. it's giving petite finale.

smoother automatically analyses different seqids separately. no mixing, no crossover, each one gets its own moment ✨

Output: 4 columns, and here they are in order:

1. seqid
2. window start
2. window end
3. averaged score

not me leaving the numbering exactly like the original 😭 two number 2's. it's iconic, we're keeping it, that's canon now.

• f,file — required: argument is a file created by GPAT++
• o,format — required: argument is the format of the input file, and it is case sensitive (watch those caps, bestie). available format options:
  • wcFst
  • pFst
  • bFst
  • iHS
  • xpEHH
  • abba-baba
  • col3
• w,window — optional: argument is the size of the genomic window in base pairs (default 5000)
• s,step — optional: argument is the window step size in base pairs (default 1000)
• t,truncate — optional: flag — end last window at last position (zero based)

Type: transformation 🌈

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💀 EXIT VALUES 💀

• 0 — Success 🎀
• not 0 — Failure 🙈

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🔥 SEE ALSO 🔥

• vcflib(1)

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👑 OTHER 👑

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.

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and that's the whole page babes 🫶 this was smoother from smoother (vcflib), no cap, go forth and smooth those windows 💖✨🌸