1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
|
% VCFALLELICPRIMITIVES(1) vcfallelicprimitives (vcflib) | vcfallelicprimitives (VCF transformation)
% Erik Garrison, Pjotr Prins and other vcflib contributors
# NAME
vcfallelicprimitives - Converts stdin or given VCF file and reduces alleles.
# SYNOPSIS
**vcfallelicprimitives**
# DESCRIPTION
**vcfallelicprimitives** converts stdin or given VCF file to tab-delimited format,
Realign reference and alternate alleles with WFA, 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.
Note that this tool is considered legacy and will emit a warning! Use
[vcfwave](./vcfwave.md) instead.
## Options
-h, --help
: shows help message and exits.
See more below.
# EXIT VALUES
**0**
: Success
**not 0**
: Failure
# EXAMPLES
<!--
>>> from rtest import run_stdout, head, cat, sh
-->
```
>>> 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:
```python
>>> 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 adjusts the genotypes accordingly splitting into two records using the original (but arguably OBSOLETE) SW algorithm:
```python
>>> 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 different result
```
1$10158244:CCCCCACCCCCAC/C
2$10158244:CCCCCACCCCCACC/C
3$10158245:CCCCACCCCCACC/C
4$10158251:CCCCACC/C
5$10158256:CC/C
```
```python
>>> 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
```
## Source code
[vcfallelicprimitives.cpp](../../src/vcfallelicprimitives.cpp)
## Regression tests
Note the wave front version has no problem with longer sequences:
```python
# ./vcfallelicprimitives -a SW -m -L 1000 ../samples/grch38#chr8_36353854-36453166.vcf > ../test/data/regression/vcfallelicprimitives_5.vcf
>>> run_stdout("vcfallelicprimitives -a SW -m -L 1000 ../samples/grch38#chr8_36353854-36453166.vcf", ext="vcf")
output in <a href="../data/regression/vcfallelicprimitives_5.vcf">vcfallelicprimitives_5.vcf</a>
# ./vcfallelicprimitives -a SW -m -L 1000 ../samples/grch38#chr4_10083863-10181258.vcf > ../test/data/regression/vcfallelicprimitives_6.vcf
/regression/vcfallelicprimitives_6.vcf
>>> run_stdout("vcfallelicprimitives -a SW -m -L 1000 ../samples/grch38#chr4_10083863-10181258.vcf", ext="vcf")
output in <a href="../data/regression/vcfallelicprimitives_6.vcf">vcfallelicprimitives_6.vcf</a>
# ./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 <a href="../data/regression/vcfallelicprimitives_7.vcf">vcfallelicprimitives_7.vcf</a>
# ./vcfallelicprimitives -m ../samples/grch38#chr4_10083863-10181258.vcf > ../test/data/regression/vcfallelicprimitives_8.vcf
>>> run_stdout("vcfallelicprimitives -m ../samples/grch38#chr4_10083863-10181258.vcf", ext="vcf")
output in <a href="../data/regression/vcfallelicprimitives_8.vcf">vcfallelicprimitives_8.vcf</a>
```
Another diff example where the first is SW and the second WFA2 showing:
```python
>>> 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|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 .|. .
```
shows how WFA2 is doing a better job at taking things apart.
Even so, this record is wrong. From 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 GTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAGCATCCCAAGTGATGTAG+}
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 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
```
Let's look at some longer sequences:
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|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
```
# vcfwave issue
Now where does the result TAGAATCCCAATTGATGG come from?
```
Original input record (see 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):
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 (see test/data/regression/vcfwave_5.vcf):
10134515 GAGAATCCCAATTGATGG TAGAATCCCAATTGATGG,G
10134518 A C
10134526 T G
10134532 G T
```
Now where does TAGAATCCCAATTGATGG come from?
Output produced by test/tests/realign.py
# LICENSE
Copyright 2011-2024 (C) Erik Garrison, Pjotr Prins and vcflib contributors. MIT licensed.
|
