VCFALL...ITIVES(1)

📦

version 1.0.12 · 3 versions

1.0.12 · debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking (latest)
1.0.9 · ubuntu noble
1.0.3 · debian bookworm, ubuntu jammy

, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

okay so welcome to VCFALL...ITIVES(1) bestie 🫶 — this is the manual page for vcfallelicprimitives, a lil VCF transformation tool that is lowkey iconic and highkey legacy. grab a boba, we're going in 🧋✨

🎀 NAME 🎀

vcfallelicprimitives — converts stdin or a given VCF file and reduces alleles. periodt. 💅

🦋 SYNOPSIS 🦋

vcfallelicprimitives

✨ DESCRIPTION ✨

okay so the vibe here is: vcfallelicprimitives takes stdin or a given VCF file and converts it to tab-delimited format. she's a converter, she's a decomposer, she's doing the absolute most and we love her for it.

then she realigns the reference and alternate alleles with WFA, parsing out the primitive alleles into multiple VCF records. the new records get IDs that reference the source record ID (so you never lose the receipts 💖). genotypes are handled, don't even stress. and deletion alleles? those will result in haploid (missing allele) genotypes. not me turning your cute diploid into a haploid 😭.

🚨 BIG SIS WARNING 🚨 this tool is considered legacy and it will emit a warning! use vcfwave instead. fr fr, i'm not playing.

🔧 Options 🔧

-h, --help — shows the help message and exits. that's it, that's the whole thing. ✨

See more below. 👀

🚪 EXIT VALUES 🚪

0 — Success. she ate and left no crumbs. 💖
not 0 — Failure. we don't talk about it. 💀

🌈 EXAMPLES 🌈

bestie this is where it gets good. here's what the help looks like:

>>> head("vcfallelicprimitives -h",29)
>
usage: ./vcfallelicprimitives [options] [file]
>
WARNING: this tool is considered legacy and is only retained for older
workflows.  It will emit a warning!  Even though it can use the WFA
you should use [vcfwave](./vcfwave.md) instead.
>
Realign reference and alternate alleles with SW or WF, parsing out
the primitive alleles into multiple VCF records. New records have IDs
that reference the source record ID.  Genotypes are handled. Deletion
alleles will result in haploid (missing allele) genotypes.
>
options:
    -a, --algorithm TYPE    Choose algorithm SW (Smith-Waterman) or WF wavefront
                            (default: WF)
    -m, --use-mnps          Retain MNPs as separate events (default: false).
    -t, --tag-parsed FLAG   Annotate decomposed records with the source record
                            position (default: ORIGIN).
    -L, --max-length LEN    Do not manipulate records in which either the ALT or
                            REF is longer than LEN (default: unlimited).
    -k, --keep-info         Maintain site and allele-level annotations when
                            decomposing.  Note that in many cases,
                            such as multisample VCFs, these won't be
                            valid post decomposition.  For biallelic
                            loci in single-sample VCFs, they should be
                            used with caution.
    -d, --debug             debug mode.
>
Type: transformation

vcfallelicprimitives picks complex regions and simplifies nested alignments. for example, look at this mess:

>>> sh("grep 10158243 ../samples/10158243.vcf")
grch38#chr4     10158243        >3655>3662      ACCCCCACCCCCACC ACC,AC,ACCCCCACCCCCAC,ACCCCCACC,ACA     60      .       AC=64,3,2,3,1;AF=0.719101,0.0337079,0.0224719,0.0337079,0.011236;AN=89;AT=>3655>3656>3657>3658>3659>3660>3662,>3655>3656>3660>3662,>3655>3660>3662,>3655>3656>3657>3658>3660>3662,>3655>3656>3657>3660>3662,>3655>3656>3661>3662;NS=45;LV=0     GT      0|0     1|1     1|1     1|0     5|1     0|4     0|1     0|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     4|3     1|1     1|1     1|1     1|0     1|0     1|0     1|0     1|1     1|1     1|4     1|1     1|1     3|0     1|0     1|1     0|1     1|1     1|1     2|1     1|2     1|1     1|1     0|1     1|1     1|1     1|0     1|2     1|1     0

after aligning, it reduces into two records with variant alleles:

10158243:ACCCCCA/A
10158243:ACCCCCACCCC/A
10158243:ACCCCCACCCCCA/A
10158243:ACCCCCACCCCCAC/A

10158255:AC/A
10158255:ACC/A

and it adjusts the genotypes accordingly, splitting into two records using the original (but arguably OBSOLETE 👵) SW algorithm:

>>> sh("../build/vcfallelicprimitives -a SW -m -L 1000 ../samples/10158243.vcf|grep -v ^\#")
grch38#chr4     10158243        >3655>3662_1    ACCCCCACCCCCAC  ACCCCCAC,ACAC,AC,A      60      .       AC=3,1,64,3;AF=0.0337079,0.011236,0.719101,0.0337079;LEN=6,10,12,13;ORIGIN=grch38#chr4:10158243,grch38#chr4:10158243,grch38#chr4:10158243,grch38#chr4:10158243;TYPE=del,del,del,del     GT      0|0     3|3     3|3     3|0     2|3     0|1     0|3     0|3     3|3     3|3     3|3     3|3     3|3     3|3     3|3     1|0     3|3     3|3     3|3     3|0     3|0     3|0     3|0     3|3     3|3     3|1     3|3     3|3     0|0     3|0     3|3     0|3     3|3     3|3     4|3     3|4     3|3     3|3     0|3     3|3     3|3     3|0     3|4     3|3     0
grch38#chr4     10158255        >3655>3662_2    ACC     AC,A    60      .       AC=2,1;AF=0.0224719,0.011236;LEN=1,2;ORIGIN=grch38#chr4:10158243,grch38#chr4:10158243;TYPE=del,del      GT      0|0     .|.     .|.     .|0     2|.     0|0     0|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     0|1     .|.     .|.     .|.     .|0     .|0     .|0     .|0     .|.     .|.     .|0     .|.     .|.     1|0     .|0     .|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     0|.     .|.     .|.     .|0     .|.     .|.     0

with the default wavefront algorithm we get a whole different result 👀:

1$10158244:CCCCCACCCCCAC/C
2$10158244:CCCCCACCCCCACC/C
3$10158245:CCCCACCCCCACC/C
4$10158251:CCCCACC/C
5$10158256:CC/C

>>> sh("../build/vcfallelicprimitives -m -L 1000 ../samples/10158243.vcf|grep -v ^\#")
grch38#chr4     10158244        >3655>3662_1    CCCCCACCCCCACC  CC,C    60      .       AC=1,3;AF=0.011236,0.0337079;LEN=12,13;ORIGIN=grch38#chr4:10158243,grch38#chr4:10158243;TYPE=del,del    GT      0|0     0|0     0|0     0|0     1|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     2|0     0|2     0|0     0|0     0|0     0|0     0|0     0|0     0|2     0|0     0
grch38#chr4     10158245        >3655>3662_2    CCCCACCCCCACC   C       60      .       AC=64;AF=0.719101;LEN=12;ORIGIN=grch38#chr4:10158243;TYPE=del   GT      0|0     1|1     1|1     1|0     .|1     0|0     0|1     0|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     0|0     1|1     1|1     1|1     1|0     1|0     1|0     1|0     1|1     1|1     1|0     1|1     1|1     0|0     1|0     1|1     0|1     1|1     1|1     .|1     1|.     1|1     1|1     0|1     1|1     1|1     1|0     1|.     1|1     0
grch38#chr4     10158251        >3655>3662_3    CCCCACC C       60      .       AC=3;AF=0.0337079;LEN=6;ORIGIN=grch38#chr4:10158243;TYPE=del    GT      0|0     .|.     .|.     .|0     .|.     0|1     0|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     1|0     .|.     .|.     .|.     .|0     .|0     .|0     .|0     .|.     .|.     .|1     .|.     .|.     0|0     .|0     .|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     0|.     .|.     .|.     .|0     .|.     .|.     0
grch38#chr4     10158256        >3655>3662_4    CC      C       60      .       AC=2;AF=0.0224719;LEN=1;ORIGIN=grch38#chr4:10158243;TYPE=del    GT      0|0     .|.     .|.     .|0     .|.     0|.     0|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     .|1     .|.     .|.     .|.     .|0     .|0     .|0     .|0     .|.     .|.     .|.     .|.     .|.     1|0     .|0     .|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     0|.     .|.     .|.     .|0     .|.     .|.     0
grch38#chr4     10158257        >3655>3662_5    C       A       60      .       AC=1;AF=0.011236;LEN=1;ORIGIN=grch38#chr4:10158243;TYPE=snp     GT      0|0     .|.     .|.     .|0     .|.     0|.     0|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     .|.     .|0     .|0     .|0     .|0     .|.     .|.     .|.     .|.     .|.     .|0     .|0     .|.     0|.     .|.     .|.     .|.     .|.     .|.     .|.     0|.     .|.     .|.     .|0     .|.     .|.     0

and here are some more regression runs, for the girls who love a snapshot test 💖:

./vcfallelicprimitives -a SW -m -L 1000 ../sam‐
       ples/grch38#chr8_36353854-36453166.vcf > ../test/data/regression/vcfall‐
       elicprimitives_5.vcf
                            run_stdout("vcfallelicprimitives -a SW -m -L 1000
                            ../samples/grch38#chr8_36353854-36453166.vcf",
                            ext="vcf") output in vcfallelicprimitives_5.vcf

./vcfallelicprimitives -a SW -m -L 1000 ../sam‐
       ples/grch38#chr4_10083863-10181258.vcf > ../test/data/regression/vcfall‐
       elicprimitives_6.vcf
       /regression/vcfallelicprimitives_6.vcf >>> run_stdout("vcfallelicprimi‐
       tives -a SW -m -L 1000 ../samples/grch38#chr4_10083863-10181258.vcf",
       ext="vcf") output in vcfallelicprimitives_6.vcf

./vcfallelicprimitives -L 10000 -m ../samples/grch38#chr8_36353854-36453166.vcf
       > ../test/data/regression/vcfallelicprimitives_7.vcf
                            run_stdout("vcfallelicprimitives -L 10000 -m
                            ../samples/grch38#chr8_36353854-36453166.vcf",
                            ext="vcf") output in vcfallelicprimitives_7.vcf

okay that's the tea so far bestie, but we are so not done — there is literally more coming, don't touch that dial 💅

./vcfallelicprimitives -m ../samples/grch38#chr4_10083863-10181258.vcf >
       ../test/data/regression/vcfallelicprimitives_8.vcf
                            run_stdout(“vcfallelicprimitives -m ../sam‐
                            ples/grch38#chr4_10083863-10181258.vcf”, ext=“vcf”)
                            output in vcfallelicprimitives_8.vcf

so that's the run that ✨made✨ the regression file, bestie — run_stdout with ext="vcf", and the output lands in vcfallelicprimitives_8.vcf. 💖

Another diff example, and the first one here is SW while the second is WFA2, showing:

>>> sh("diff data/regression/vcfallelicprimitives_6.vcf data/regression/vcfallelicprimitives_8.vcf|tail -6")
1670c1680,1682
< grch38#chr4   10180508        >4593>4597_1    CTT     CTTT,CT,C       60      .       AC=7,47,1;AF=0.0786517,0.52809,0.011236;LEN=1,1,2;ORIGIN=grch38#chr4:10180508,grch38#chr4:10180508,grch38#chr4:10180508;TYPE=ins,del,del        GT      2|0     0|2     2|2     2|0     2|2     0|0     0|2     0|2     2|2     2|2     2|0     2|0     0|2     2|0     2|2     2|0     2|2     2|2     2|2     2|0     0|1     0|0     2|1     2|2     0|2     2|2     2|0     0|2     0|3     2|1     0|2     0|0     2|0     1|2     2|2     0|1     2|2     0|0     0|0     1|0     0|1     2|0     0|0     2|2     2
---
> grch38#chr4   10180508        >4593>4597_1    CTT     C       60      .       AC=1;AF=0.011236;LEN=2;ORIGIN=grch38#chr4:10180508;TYPE=del     GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0
> grch38#chr4   10180509        >4593>4597_2    TT      T       60      .       AC=47;AF=0.52809;LEN=1;ORIGIN=grch38#chr4:10180508;TYPE=del     GT      1|0     0|1     1|1     1|0     1|1     0|0     0|1     0|1     1|1     1|1     1|0     1|0     0|1     1|0     1|1     1|0     1|1     1|1     1|1     1|0     0|0     0|0     1|0     1|1     0|1     1|1     1|0     0|1     0|.     1|0     0|1     0|0     1|0     0|1     1|1     0|0     1|1     0|0     0|0     0|0     0|0     1|0     0|0     1|1     1
> grch38#chr4   10180510        >4593>4597_3    T       TT      60      .       AC=7;AF=0.0786517;LEN=1;ORIGIN=grch38#chr4:10180508;TYPE=ins    GT      .|0     0|.     .|.     .|0     .|.     0|0     0|.     0|.     .|.     .|.     .|0     .|0     0|.     .|0     .|.     .|0     .|.     .|.     .|.     .|0     0|1     0|0     .|1     .|.     0|.     .|.     .|0     0|.     0|.     .|1     0|.     0|0     .|0     1|.     .|.     0|1     .|.     0|0     0|0     1|0     0|1     .|0     0|0     .|.     .

which literally shows how WFA2 is doing a better job at taking things apart. ate, no crumbs 💅

Even so… this record is wrong, bestie, I'm so serious 😭. Straight out of grch38#chr4_10083863-10181258.vcf:

Differences between WFA and biWFA:

wdiff vcfallelicprimitives_8.vcf vcfwave_5.vcf
grch38#chr4     10134337        >2103>2106_1    [-TTTTG AGGCA-] {+TTTTGGTGTACTGCCT      AGGCAGTACACCAAAA+}
grch38#chr4     10134492        >2125>2211_3    [-TTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTG    GTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTG-]     {+TTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAG     GTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAG+}
grch38#chr4     10134498
grch38#chr4     [-10134501      >2125>2211_5    AATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATT       CATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATT-]      {+10134500      >2125>2211_6    GAATCCCAATTGATGGAG      G+}     60      .       [-AC=1;AF=0.011236;INV=0,0;LEN=17;ORIGIN=grch38#chr4:10134484;TYPE=complex-]    {+AC=1;AF=0.011236;INV=0;LEN=17;ORIGIN=grch38#chr4:10134484;TYPE=del+}
  GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
     0|0     0|1     0|0     0|0     0|0     0
grch38#chr4     {+10134518      >2125>2211_7    AATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATTGATGGAGAATCCCAATT        CATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATTGATGGAGCATCCCAATT        60      .       AC=1;AF=0.011236;INV=0;LEN=112;ORIGIN=grch38#chr4:10134484;TYPE=mnp     GT      0|0     0|0     0|0     0|0     0|0     0|0
     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     0|0     0|0
     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     0

Another problem case, this one fixed with fb7365b07f832bcfcc6ddb693ddfc4a01a25cfbb 🫶:

grch38#chr8_36353854-36453166.vcf:grch38#chr8   36382847        >721>726        GT      GC,AC

SW 🌸

vcfallelicprimitives_5.vcf:grch38#chr8  36382847        >721>726_1      GT      AC
vcfallelicprimitives_5.vcf:grch38#chr8  36382848        >721>726_2      T       C

WF ✨

vcfwave_4.vcf:grch38#chr8       36382847        >721>726_1      G       A

okay now let's look at some longer sequences, bestie, this is where it gets spicy 🌶️

The original 👑

grch38#chr4_10083863-10181258.vcf:grch38#chr4   10134514        >2136>2148      GGAGAATCCCAATTGATGG     GTAGCATCCCAAGTGATGT,GTAGAATCCCAATTGATGT,GGAGCATCCCAATTGATGG,GG     60      .       AC=11,7,1,3;AF=0.125,0.0795455,0.0113636,0.0340909;AN=88;AT=>2136>2138>2139>2141>2142>2144>2145>2147>2148,>2136>2137>2139>2140>2142>2143>2145>2146>2148,>2136>2137>2139>2141>2142>2144>2145>2146>2148,>2136>2138>2139>2140>2142>2144>2145>2147>2148,>2136>2138>2148;NS=45;LV=1;PS=>2125>2211     GT      0|1     1|0     0|0     0|1     0|0     1|0     1|01|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     2|2     0|0     4|0     0|0     0|1     0|10|1     0|2     0|0     4|0     0|2     0|0     0|0     2|0     0|0     0|0     0|0     0|0     0|0     2|04|1     0|0     0|0     0|0     0|0     0|3     0|0     0|2     0|0     1
# translates to SW
vcfallelicprimitives_6.vcf:grch38#chr4  10134514        >2136>2148_1    GGAGAATCCCAATTGATG      G       60.AC=3;AF=0.0340909;LEN=17;ORIGIN=grch38#chr4:10134514;TYPE=del   GT      0|0     0|0     0|0     0|0     0|00|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     1|0     0|00|0     0|0     0|0     0|0     0|0     1|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0     0|0     1|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0
vcfallelicprimitives_6.vcf:grch38#chr4  10134515        >2136>2148_2    GAGAATCCCAATTGATGG      TAGAATCCCAATTGATGT,TAGCATCCCAAGTGATGT      60      .       AC=7,11;AF=0.0795455,0.125;LEN=18,18;ORIGIN=grch38#chr4:10134514,grch38#chr4:10134514;TYPE=mnp,mnp GT      0|2     2|0     0|0     0|2     0|0     2|0     2|0     2|00|0     0|0     0|0     0|0     0|0     0|.     0|0     1|1     0|0     .|0     0|0     0|2     0|2     0|20|1     0|0     .|0     0|1     0|0     0|0     1|0     0|0     0|0     0|0     0|0     0|0     1|0     .|20|0     0|0     0|0     0|0     0|0     0|0     0|1     0|0     2
vcfallelicprimitives_6.vcf:grch38#chr4  10134518        >2136>2148_3    AATCCCAATTGATGG CATCCCAATTGATGG 60.AC=1;AF=0.0113636;LEN=15;ORIGIN=grch38#chr4:10134514;TYPE=mnp   GT      0|0     0|0     0|0     0|0     0|00|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     .|0     0|00|0     0|0     0|0     0|0     0|0     .|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0     0|0     .|0     0|0     0|0     0|0     0|0     0|1     0|0     0|0     0|0     0
# and WFA
vcfallelicprimitives_8.vcf:grch38#chr4  10134515        >2136>2148_1    GAGAATCCCAATTGATGG      TAGCATCCCAAGTGATGG,TAGAATCCCAATTGATGG,G    60      .       AC=11,7,3;AF=0.125,0.0795455,0.0340909;LEN=14,16,17;ORIGIN=grch38#chr4:10134514,grch38#chr4:10134514,grch38#chr4:10134514;TYPE=mnp,mnp,del GT      0|1     1|0     0|00|1     0|0     1|0     1|0     1|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     2|2     0|03|0     0|0     0|1     0|1     0|1     0|2     0|0     3|0     0|2     0|0     0|0     2|0     0|0     0|00|0     0|0     0|0     2|0     3|1     0|0     0|0     0|0     0|0     0|0     0|0     0|2     0|0     1
vcfallelicprimitives_8.vcf:grch38#chr4  10134518        >2136>2148_2    AATCCCAATTGATG  CATCCCAATTGATG  60.AC=1;AF=0.0113636;LEN=14;ORIGIN=grch38#chr4:10134514;TYPE=mnp   GT      0|0     0|0     0|0     0|0     0|00|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|.     0|0     0|0     0|0     .|0     0|00|0     0|0     0|0     0|0     0|0     .|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0     0|0     .|0     0|0     0|0     0|0     0|0     0|1     0|0     0|0     0|0     0

To describe the bug we get for grch38#chr4 10134514 (or: original, sw:, wf:). It was fixed with commit fb7365b07f832bcfcc6ddb693ddfc4a01a25cfbb.

ori: GGAGAATCCCAATTGATGG->GG
sw:  GGAGAATCCCAATTGATG ->G
wf:   GAGAATCCCAATTGATGG->G
fix:  GAGAATCCCAATTGATGG->G

ori: GGAGAATCCCAATTGATGG->GTAGCATCCCAAGTGATGT
sw:   GAGAATCCCAATTGATGG-> TAGAATCCCAATTGATGT
wf:   GAGAATCCCAATTGATGG-> TAGAATCCCAATTGATGG <-
fix:  GAGAATCCCAATTGATGG-> TAGAATCCCAATTGATGT

ori: GGAGAATCCCAATTGATGG ->GTAGAATCCCAATTGATGT
sw:   GAGAATCCCAATTGATGG -> TAGCATCCCAAGTGATGT
wf:   GAGAATCCCAATTGATGG -> TAGCATCCCAAGTGATGG <-
fix:   GAGAATCCCAATTGATGG-> TAGCATCCCAAGTGATGT
      GAGAATCCCAATTGATGG-> TAGAATCCCAATTGATGG

ori: GGAGAATCCCAATTGATGG->GGAGCATCCCAATTGATGG
sw:    AATCCCAATTGATGG->      CATCCCAATTGATGG
wf:    AATCCCAATTGATG ->      CATCCCAATTGATG
fix:   AATCCCAATTGATGG->      CATCCCAATTGATGG
      A                      C

see those little <- arrows? yeah, that's the bug pointing at itself 💀 the fix: lines are what it's supposed to be, and the commit fb7365b07f832bcfcc6ddb693ddfc4a01a25cfbb is the glow-up that made it right 💖

Okay so bestie, let's talk about this vcfwave issue because it's a whole mood. 🧚 You look at your output and you're like... TAGAATCCCAATTGATGG?? Where did THAT come from?? Not me spiraling over a string of nucleotides at 2am. 💀 Let's trace it together.

Original input record — peep samples/10134514.vcf:

10134514 GGAGAATCCCAATTGATGG     GTAGCATCCCAAGTGATGT,GTAGAATCCCAATTGATGT,GGAGCATCCCAATTGATGG,GG

WF CIGARs:

10134514:1M1X2M1X7M1X5M1X:GGAGAATCCCAATTGATGG,GTAGCATCCCAAGTGATGT
10134514:1M1X16M1X:GGAGAATCCCAATTGATGG,GTAGAATCCCAATTGATGT
10134514:4M1X14M:GGAGAATCCCAATTGATGG,GGAGCATCCCAATTGATGG
10134514:2M17D:GGAGAATCCCAATTGATGG,GG

Decomposed alleles (return from parsedAlternates) — this is the part that's giving ✨algorithm✨:

GGAGAATCCCAATTGATGG 10134514 GGAGAATCCCAATTGATGG -> GGAGAATCCCAATTGATGG
GGAGCATCCCAATTGATGG 10134514 GGAG -> GGAG
GGAGCATCCCAATTGATGG 10134518 A -> C
GGAGCATCCCAATTGATGG 10134519 ATCCCAATTGATGG -> ATCCCAATTGATGG
GTAGAATCCCAATTGATGT 10134514 G -> G
GTAGAATCCCAATTGATGT 10134515 G -> T
GTAGAATCCCAATTGATGT 10134516 AGAATCCCAATTGATG -> AGAATCCCAATTGATG
GTAGAATCCCAATTGATGT 10134532 G -> T
GTAGCATCCCAAGTGATGT 10134514 G -> G
GTAGCATCCCAAGTGATGT 10134515 G -> T
GTAGCATCCCAAGTGATGT 10134516 AG -> AG
GTAGCATCCCAAGTGATGT 10134518 A -> C
GTAGCATCCCAAGTGATGT 10134519 ATCCCAA -> ATCCCAA
GTAGCATCCCAAGTGATGT 10134526 T -> G
GTAGCATCCCAAGTGATGT 10134527 TGATG -> TGATG
GTAGCATCCCAAGTGATGT 10134532 G -> T

Final result — this is the glow-up, see test/data/regression/vcfwave_5.vcf:

10134515 GAGAATCCCAATTGATGG      TAGAATCCCAATTGATGG,G
10134518 A                       C
10134526 T                       G
10134532 G                       T

And the question that started all of this, one more time, no cap:

Now where does TAGAATCCCAATTGATGG come from?

The output was produced by test/tests/realign.py. 🦋

💖 LICENSE 💖

🫶 AUTHORS 🫶

Erik Garrison, Pjotr Prins and other vcflib contributors. Absolute legends, honestly. 👑

And that's the whole page, bestie! 🎀 It's vcfallelicprimitives (vcflib), aka VCFALL...ITIVES(1) — shoutout to the source and the version tag, mwah. Now go realign something iconic. 💖✨

📦 where this page comes from

debian trixie: libvcflib-tools 1.0.12+dfsg-1 · MIT
ubuntu questing: libvcflib-tools 1.0.12+dfsg-1
ubuntu resolute: libvcflib-tools 1.0.12+dfsg-2 · MIT
ubuntu stonking: libvcflib-tools 1.0.12+dfsg-2 · MIT
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-18: a language model's rewrite of the original, under its terms