Mercurial > repos > bgruening > vt

annotate vt_decompose.xml @ 0:26babe3a66f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
author bgruening
date Sat, 04 Jun 2016 10:41:29 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
1 <tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
2 <description>decomposes multiallelic variants into biallelic ones</description>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
3 <macros>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
4 <import>vt_macros.xml</import>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
5 <token name="@BINARY@">decompose</token>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
6 </macros>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
8 <expand macro="stdio" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
9 <expand macro="version_command" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
10 <command>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
11 <![CDATA[
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
12
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
13 ln -s "${ infile }" infile.vcf &&
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
14
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
15
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
16 vt @BINARY@
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
17 #if str($output_format) == 'bcf':
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
18 -o decompose.bcf
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
19 #else:
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
20 -o decompose.vcf
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
21 #end if
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
22 $s
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
23 infile.vcf
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
24
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
25 &&
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
26 ## For some reason, the file move will randomly produce empty files.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
27 ## Wait two seconds to let the system close file handlers and clean up.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
28 sleep 2
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
29 &&
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
30
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
31 #if str($output_format) == 'bcf':
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
32 mv decompose.bcf "${ outfile }";
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
33 #else:
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
34 mv decompose.vcf "${ outfile }";
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
35 #end if
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
36
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
37 ]]>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
38 </command>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
39 <inputs>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
40 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
41
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
42 <param argument="-s" type="boolean" truevalue="-s" falsevalue=""
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
43 selected="false" label="Smart decomposition"
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
44 help="Splits up INFO and GENOTYPE fields that have number counts of R and A appropriately."/>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
45
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
46 <param name="output_format" type="select" label="Choose the output format" help="">
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
47 <option value="bcf">BCF</option>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
48 <option value="vcf" selected="true">VCF</option>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
49 </param>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
50 </inputs>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
51 <outputs>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
52 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
53 <change_format>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
54 <when input="output_format" value="bcf" format="bcf" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
55 </change_format>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
56 </data>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
57 </outputs>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
58 <tests>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
59 <test>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
60 <param name="infile" value="infile01.vcf" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
61 <output name="outfile" file="decompose_result01.vcf" ftype="vcf" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
62 </test>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
63 <test>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
64 <param name="infile" value="infile02.vcf" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
65 <param name="s" value="True" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
66 <output name="outfile" file="decompose_result02.vcf" ftype="vcf" />
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
67 </test>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
68 </tests>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
69 <help>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
70 <![CDATA[
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
71
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
72 **What it does**
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
73
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
74 Decompose multiallelic variants in a VCF file.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
75 If the VCF file has genotype fields GT,PL, GL or DP, they are modified to reflect the change in alleles.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
76 All other genotype fields are removed. The -s option will retain the fields and decompose fields of counts R and A accordingingly.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
77
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
78 Decomposition and combining variants is a complex operation where the correctness is dependent on:
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
79
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
80 * whether the observed variants are seen in the same sample
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
81 * if same sample, whether they are homozygous or heterozygous
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
82 * if both heterozygous, whether they are in the same haplotype or not (if known)
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
83
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
84 and one should be aware of the issues in handling variants resulting from such operations.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
85 The original purpose of this tool is to allow for allelic comparisons between call sets.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
86
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
87 Standard option:
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
88
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
89 Before decomposition
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
90
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
91 .. code::
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
92
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
93 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
94 1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
95
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
96 After decomposition
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
97
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
98 .. code::
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
99
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
100 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
101 1 3759889 . TA TAA . PASS OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
102 1 3759889 . TA TAAA . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
103 1 3759889 . TA T . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
104
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
105
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
106 One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
107
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
108
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
109 With **-s** option:
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
110
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
111 Before decomposition
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
112
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
113 .. code::
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
114
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
115 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
116 1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
117
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
118 After decomposition
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
119
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
120 .. code::
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
121
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
122 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
123 1 3759889 . TA TAA . PASS AF=0.342;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
124 1 3759889 . TA TAAA . . AF=0.173;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
125 1 3759889 . TA T . . AF=0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
126
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
127 In general, you should recompute fields that involves alleles after decomposition. Information is generally lost after vertically decomposing a variant, so care should be taken in interpreting the resultant values.
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
128
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
129 @CITATION@
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
130 ]]>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
131 </help>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
132 <expand macro="citations"/>
26babe3a66f1 planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
bgruening
parents:
diff changeset
133 </tool>