VCFLENGTH(1)

✨ vcflength ✨

okay bestie, so this is vcflength from the vcflib crew — it's a VCF transformation tool, and honestly? it does exactly one thing and it does it flawlessly 💅

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🌸 NAME 🌸

vcflength — the little tool that adds length info to your VCF, no cap

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🎀 SYNOPSIS 🎀

vcflength

that's it. that's the whole synopsis. she takes no args on the command line in the synopsis sense, she just reads your VCF and pops off 🫶

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✨ DESCRIPTION ✨

Add length info field 💖

(yeah that's the whole vibe — she goes through your variants and adds length, length.alt and length.ref info fields. periodt.)

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🦋 EXAMPLES 🦋

Example:

**vcflength** samples/sample.vcf
##fileformat=VCFv4.0
(...)
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003
19      111     .       A       C       9.6     .       length=0;length.alt=1;length.ref=1      GT:HQ   0|0:10,10  0|0:10,10       0/1:3,3
19      112     .       A       G       10      .       length=0;length.alt=1;length.ref=1      GT:HQ   0|0:10,10  0|0:10,10       0/1:3,3
20      14370   rs6054257       G       A       29      PASS    AF=0.5;DP=14;NS=3;length=0;length.alt=1;length.ref=1;DB;H2 GT:GQ:DP:HQ     0|0:48:1:51,51  1|0:48:8:51,51  1/1:43:5:.,.
20      17330   .       T       A       3       q10     AF=0.017;DP=11;NS=3;length=0;length.alt=1;length.ref=1     GT:GQ:DP:HQ     0|0:49:3:58,50  0|1:3:5:65,3    0/0:41:3:.,.
20      1110696 rs6040355       A       G,T     67      PASS    AA=T;AF=0.333,0.667;DP=10;NS=2;length=0,0;length.alt=1,1;length.ref=1;DB   GT:GQ:DP:HQ     1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4:.,.
20      1230237 .       T       .       47      PASS    AA=T;DP=13;NS=3;length=0;length.alt=1;length.ref=1GT:GQ:DP:HQ      0|0:54:.:56,60  0|0:48:4:51,51  0/0:61:2:.,.
20      1234567 microsat1       G       GA,GAC  50      PASS    AA=G;AC=3,1;AN=6;DP=9;NS=3;length=1,2;length.alt=2,3;length.ref=1  GT:GQ:DP        0/1:.:4 0/2:17:2        1/1:40:3
20      1235237 .       T       .       0       .       length=0;length.alt=1;length.ref=1      GT      0/00|0     ./.
X       10      rsTest  AC      A,ATG   10      PASS    length=-1,1;length.alt=1,3;length.ref=2 GT      0 0/1      0|2

Type: transformation 🔥

bestie pls don't retype that code block by hand, it's verbatim from the manpage and your girl does not want you debugging a typo at 2am 😭

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💜 EXIT VALUES 💜

• 0 — Success 🎉 she ate, everything's fine, go drink some water
• not 0 — Failure 💀 something went sideways, the vibe check failed

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👑 SEE ALSO 👑

• vcflib(1) — the whole squad, iykyk

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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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okay that's the whole page bestie, you're basically a vcflength expert now 🫶 this was vcflength from the vcflib package — mwah, go forth and annotate your lengths, no cap 💅✨