VCFPARSEALTS(1)

💖 NAME 💖

okay so bestie, meet vcfparsealts — she's a whole vibe from the vcfparsealts (VCF statistics) manual section, and she's here to break down your alternate alleles like it's nothing 💅

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✨ SYNOPSIS ✨

vcfparsealts

that's it. no flags, no drama, she just is 🫶

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🌸 DESCRIPTION 🌸

This is the alternate allele parsing method. The way it works is pairwise alignment of REF and ALTs, and that's how it figures out the component allelic primitives for each alternate allele. like, it's not just looking at the ALT as one big blob — it's decomposing it, atom by atom, bestie. iconic behavior honestly 🧚✨

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🦋 EXAMPLES 🦋

Example:

**vcfparsealts** samples/sample.vcf
##fileformat=VCFv4.0
(...)
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003
19      111     .       A       C       9.6     .       .       GT:HQ   0|0:10,10       0|0:10,10       0/1:3,3
 ( A :: 111 A -> A;  )  ( C :: 111 A -> C;  )
19      112     .       A       G       10      .       .       GT:HQ   0|0:10,10       0|0:10,10       0/1:3,3
 ( A :: 112 A -> A;  )  ( G :: 112 A -> G;  )
20      14370   rs6054257       G       A       29      PASS    AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ     0|0:48:1:51,51     1|0:48:8:51,51  1/1:43:5:.,.
 ( A :: 14370 G -> A;  )  ( G :: 14370 G -> G;  )
20      17330   .       T       A       3       q10     AF=0.017;DP=11;NS=3     GT:GQ:DP:HQ     0|0:49:3:58,50     0|1:3:5:65,3    0/0:41:3:.,.
 ( A :: 17330 T -> A;  )  ( T :: 17330 T -> T;  )
20      1110696 rs6040355       A       G,T     67      PASS    AA=T;AF=0.333,0.667;DP=10;NS=2;DB       GT:GQ:DP:HQ        1|2:21:6:23,27  2|1:2:0:18,2    2/2:35:4:.,.
 ( A :: 1110696 A -> A;  )  ( G :: 1110696 A -> G;  )  ( T :: 1110696 A -> T;  )
20      1230237 .       T       .       47      PASS    AA=T;DP=13;NS=3 GT:GQ:DP:HQ     0|0:54:.:56,60  0|0:48:4:51,51     0/0:61:2:.,.
 ( . :: 1230237 T -> .;  )  ( T :: 1230237 T -> T;  )
20      1234567 microsat1       G       GA,GAC  50      PASS    AA=G;AC=3,1;AN=6;DP=9;NS=3      GT:GQ:DP  0/1:.:4  0/2:17:2        1/1:40:3
 ( G :: 1234567 G -> G;  )  ( GA :: 1234567 G -> G; 1234568  -> A;  )  ( GAC :: 1234567 G -> G; 1234568  -> AC;  )
20      1235237 .       T       .       0       .       .       GT      0/0     0|0     ./.
 ( . :: 1235237 T -> .;  )  ( T :: 1235237 T -> T;  )
X       10      rsTest  AC      A,ATG   10      PASS    .       GT      0       0/1     0|2
 ( A :: 10 A -> A; 11 C -> ;  )  ( AC :: 10 AC -> AC;  )  ( ATG :: 10 A -> A; 11  -> T; 11 C -> G;  )

Type: statistics

see how every ALT gets its own lil parenthetical breakdown? that's the whole point, fr fr 🔥

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💀 EXIT VALUES 💀

• 0 — Success 🎉 she ate, no notes
• not 0 — Failure 😭 something went sideways

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🌈 SEE ALSO 🌈

• vcflib(1) — the whole fam, go say hi

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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, bestie 💖 this lil manual lives in the vcflib source/version corner of the world — so go forth, parse those alts, and slay ✨🦋🌸💅