forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 2
/
meta.yml
76 lines (76 loc) · 2.56 KB
/
meta.yml
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
name: gatk4_applyvqsr
description: |
Apply a score cutoff to filter variants based on a recalibration table.
AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
Specifically, it applies filtering to the input variants based on the recalibration table produced
in the first step by VariantRecalibrator and a target sensitivity value.
keywords:
- gatk4
- variant quality score recalibration
- vcf
- vqsr
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- vcf:
type: file
description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
pattern: "*.vcf"
- vcf_tbi:
type: file
description: tabix index for the input vcf file.
pattern: "*.vcf.tbi"
- recal:
type: file
description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
pattern: "*.recal"
- recal_index:
type: file
description: Index file for the recalibration file.
pattern: ".recal.idx"
- tranches:
type: file
description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
pattern: ".tranches"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- vcf:
type: file
description: compressed vcf file containing the recalibrated variants.
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of recalibrated vcf file.
pattern: "*vcf.gz.tbi"
- versions:
type: file
description: File containing software versions.
pattern: "versions.yml"
authors:
- "@GCJMackenzie"
maintainers:
- "@GCJMackenzie"