-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathconfig.yaml
167 lines (166 loc) · 7.4 KB
/
config.yaml
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
# Ryan's dback home jetstream config file
backend: slurm
pipelines:
home: /home/rrichholt/jetstream_pipelines/
constants:
tools:
bwa_0_7_12:
module: bwa/0.7.12
version: "0.7.12"
verbose: Burrows-Wheeler Aligner v0.7.12
website: http://bio-bwa.sourceforge.net
citation: >
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60. [PMID: 19451168]
bwa_0_7_17:
module: bwa/0.7.17
version: "0.7.17"
verbose: Burrows-Wheeler Aligner v0.7.17
website: http://bio-bwa.sourceforge.net
citation: >
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60. [PMID: 19451168]
freebayes_1_2:
module: freebayes/1.2
version: "1.2"
verbose: Freebayes v1.2
website: https://github.com/ekg/freebayes
citation: >
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing.
arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
gatk_4_1_0_0:
module: gatk/4.1.0.0
version: "4.1.0.0"
verbose: Genome Analysis Toolkit v4.1.0.0
website: https://software.broadinstitute.org/gatk/
citation: >
The Genome Analysis Toolkit: a MapReduce framework for analyzing
next-generation DNA sequencing data McKenna A, Hanna M, Banks E,
Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D,
Gabriel S, Daly M, DePristo MA, 2010 GENOME RESEARCH 20:1297-303
hmmcopy_utils_1_0:
module: HMM_Copy_Utils/1.0
version: "1.0"
verbose: HMM Copy Utils v1.0
website: https://github.com/shahcompbio/hmmcopy_utils
citation: >
Daniel Lai [email protected] Department of Molecular Oncology, BC Cancer
Research Agency Date: August 02, 2011
htseq_0_6_1:
module: HTSeq/0.6.1
version: 0.6.1
verbose: HTSeq v0.6.1
website: https://htseq.readthedocs.io
citation: >
Simon Anders, Paul Theodor Pyl, Wolfgang Huber
HTSeq — A Python framework to work with high-throughput sequencing data
Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638
ichorcna_0_1_0:
module: R/3.4.1
launcher: /home/tgenref/binaries/scripts/ichorCNA/0.1.0-1d54a1f/runIchorCNA.R
version: "0.1.0-1d54a1f"
verbose: ichorCNA v0.1.0 (1d54a1f)
website: https://github.com/broadinstitute/ichorCNA
citation: >
Adalsteinsson, Ha, Freeman, et al. Scalable whole-exome sequencing of
cell-free DNA reveals high concordance with metastatic tumors. (2017)
Nature Communications Nov 6;8(1):1324. doi: 10.1038/s41467-017-00965-y
lancet_1_0_7:
module: lancet/1.0.7
version: "1.0.7"
verbose: lancet v1.0.7
website: https://github.com/nygenome/lancet
citation: >
Narzisi G, Corvelo A, Arora K, Bergmann E, Shah M, Musunuri R, Emde AK, Robine N, Vacic V,
Zody MC. Genome-wide somatic variant calling using localized colored de Bruijn graphs.
Communications Biology, Nature Research publishing, volume 1, Article number: 20, 2018
(DOI:10.1038/s42003-018-0023-9). Also available at CSHL bioRxiv 196311; 2017 (DOI: 10.1101/196311)
manta_1_4:
module: manta/1.4
version: "1.4"
verbose: Manta v1.4
website: https://github.com/Illumina/manta
citation: >
Chen, X. et al. (2016) Manta: rapid detection of structural variants and indels for germline and
cancer sequencing applications. Bioinformatics, 32, 1220-1222. doi:10.1093/bioinformatics/btv710
rstats_3_4_1:
module: R/3.4.1
version: "3.4.1"
verbose: R v3.4.1
website: https://www.r-project.org
citation: >
R Core Team (2017). R: A language and environment for statistical computing. R Foundation for
Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
samtools_1_7:
module: samtools/1.7
version: "1.7"
verbose: SAMtools v1.7
website: http://www.htslib.org
citation: >
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000
Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools,
Bioinformatics (2009) 25(16) 2078-9 [19505943]
samtools_1_9:
module: samtools/1.9
version: "1.9"
verbose: SAMtools v1.9
website: http://www.htslib.org
citation: >
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000
Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools,
Bioinformatics (2009) 25(16) 2078-9 [19505943]
salmon_0_12_0:
module: salmon/0.12.0
version: "0.12.0"
verbose: Salmon v0.12.0
website: https://combine-lab.github.io/salmon/
citation: >
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides
fast and bias-aware quantification of transcript expression. Nature Methods.
snpeff_4_3t:
module: snpEff/v4_3t
version: "4.3T"
verbose: SnpEff v4.3T
website: http://snpeff.sourceforge.net/index.html
citation: >
A program for annotating and predicting the effects of single
nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang
le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin).
2012 Apr-Jun;6(2):80-92. PMID: 22728672
star_2_6_1d:
module: STAR/2.6.1d
version: 2.6.1d
verbose: STAR v2.6.1d
website: https://github.com/alexdobin/STAR
citation: >
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P,
Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner.
Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub
2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.
star_fusion_1_5_0:
module: STAR-Fusion/1.5.0
version: 1.5.0
verbose: STAR-Fusion v1.5.0
website: https://github.com/STAR-Fusion/STAR-Fusion
citation: >
"STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
Brian Haas, Alexander Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle,
Asma Bankapur, Carrie Ganote, Thomas Doak, Natalie Pochet, Jing Sun, Catherine Wu,
Thomas Gingeras, Aviv Regev bioRxiv 120295; doi: https://doi.org/10.1101/120295"
strelka_2_9_2:
module: strelka/2.9.2
version: "2.9.2"
verbose: Strelka2 Small Variant Caller v2.9.2
website: https://github.com/Illumina/strelka
citation: >
Kim, S., Scheffler, K. et al. (2018) Strelka2: fast and accurate calling of germline and somatic
variants. Nature Methods, 15, 591-594. doi:10.1038/s41592-018-0051-x
verifybamid2_1_0_5:
module: verifybamID/1.0.5
version: 1.0.5
website: https://github.com/Griffan/VerifyBamID
citation: >
Zhang F., Flickinger M., InPSYght Psychiatric Genetics Consortium, Abecasis G., Boehnke M.,
Kang H.M.(8 November 2018)."Ancestry-agnostic estimation of DNA sample contamination from
sequence reads".bioRxiv 466268; doi: https://doi.org/10.1101/466268