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978 lines (978 loc) · 22.8 KB
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install_repository_dependencies: false
install_resolver_dependencies: false
install_tool_dependencies: false
tools:
- name: vcfcheck
owner: devteam
revisions:
- aa8e8c96ca06
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: artic_minion
owner: iuc
revisions:
- 468b90c41cde
- 6f52ebc01098
- 7021ed347f7e
- 93cfe7df7f8a
- c218cc6bf765
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: artic_guppyplex
owner: iuc
revisions:
- 00e20a06ff1e
- 311d11c4a68b
- 372def2f8fd6
- c23737f9714f
- e92767bd4412
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: manta
owner: artbio
revisions:
- 555971edd46e
- bebb4f9eba4f
- cb5691381acb
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: smgu_frameshift_deletions_checks
owner: iuc
revisions:
- 5f0d3c6f4e59
- 81f337815c1b
- 8ada4c573595
- e8971ca74398
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: cnvkit_antitarget
owner: iuc
revisions:
- b52fa1df3bc4
- f1b016247826
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: cnvkit_access
owner: iuc
revisions:
- 9f18bcf53f92
- ee93e2047dc1
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: strelka_germline
owner: iuc
revisions:
- 19481653a22f
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: sansa_annotate
owner: iuc
revisions:
- 7ca2fba4be83
- b1ca9fce4749
- fe8bc8d1e7f5
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: strelka_somatic
owner: iuc
revisions:
- edbdbc64b397
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_filter
owner: iuc
revisions:
- 74f9f312c713
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_merge
owner: iuc
revisions:
- 6c44bbc0eaa5
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_call
owner: iuc
revisions:
- c34eab9d5134
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_lr
owner: iuc
revisions:
- 97f649646cc1
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_consensus
owner: iuc
revisions:
- 147de996e34f
- 8aa352093d73
- 9a260f6fab93
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_classify
owner: iuc
revisions:
- df4300f300e4
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: delly_cnv
owner: iuc
revisions:
- 8ad49c4272ea
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfanno
owner: iuc
revisions:
- 2c526639f63c
- 4f3c5e634679
- 7b2ee758de86
- c192a2c7ef00
- ecc7758d828f
- fb20fa735dfe
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: jasminesv
owner: iuc
revisions:
- 2b62154e39c8
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: irissv
owner: iuc
revisions:
- 3242dbeea69c
- b4b6b660293a
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: snpfreqplot
owner: iuc
revisions:
- 3d0adeee3f2b
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: variant_analyzer
owner: iuc
revisions:
- 3f1dbd2c59bf
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: snpsift
owner: iuc
revisions:
- 09d6806c609e
- 0abc5513f795
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- 5fab4f81391d
- b04635ebfab0
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lumpy_sv
owner: iuc
revisions:
- 88b35d91a662
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lumpy_prep
owner: iuc
revisions:
- 80adce82354c
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lofreq_filter
owner: iuc
revisions:
- 7dfca164d2e3
- 950d1d49d678
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lofreq_call
owner: iuc
revisions:
- 4805fe3d8fda
- b11e8e9c23bf
- e1461b5c52a0
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: plink
owner: iuc
revisions:
- 16d22eee0fe3
- 2c0ac05fe240
- 9c48485bf664
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: cutesv
owner: iuc
revisions:
- 278efc44f61a
- c0f8fe52948e
- cb441f258c37
- ccc439243918
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: sniffles
owner: iuc
revisions:
- 93c4b04a0769
- ceff2f6a5368
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vardict_java
owner: iuc
revisions:
- e0734e88a104
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: control_freec
owner: iuc
revisions:
- f923c54a17ee
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: gatk4_mutect2
owner: iuc
revisions:
- 2898012c5265
- 53ce8be43212
- fb0bb7174530
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_concat
owner: iuc
revisions:
- 05f317e50e61
- 08296952d12f
- c3c930926708
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: snpeff_sars_cov_2
owner: iuc
revisions:
- 2a3a00c1fa0a
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lofreq_viterbi
owner: iuc
revisions:
- aa35ee7f3ab2
- af7e416d8176
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lofreq_alnqual
owner: iuc
revisions:
- 791f73caa0c8
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: lofreq_indelqual
owner: iuc
revisions:
- 354b534eeab7
- 426d707dfc47
- 971e07ca4456
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: seqwish
owner: iuc
revisions:
- 0c415ba215e7
- 45171c84aee1
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: odgi_viz
owner: iuc
revisions:
- 911a3517b738
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: odgi_build
owner: iuc
revisions:
- 6584dfcc7165
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vg_view
owner: iuc
revisions:
- ee62774bb5bd
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vg_deconstruct
owner: iuc
revisions:
- 76d18b1e970b
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vg_convert
owner: iuc
revisions:
- 7366704232b6
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: snippy
owner: iuc
revisions:
- 08d22d220254
- d220115f882b
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_merge
owner: iuc
revisions:
- 5b006286a458
- af163c712539
- d3286f971e89
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfselectsamples
owner: devteam
revisions:
- 2ba3b87f904f
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfannotategenotypes
owner: devteam
revisions:
- 84959112d9a6
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfdistance
owner: devteam
revisions:
- 5822b40f3037
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfflatten
owner: devteam
revisions:
- f285aa6bdcfb
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfcommonsamples
owner: devteam
revisions:
- f1852ecef841
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfannotate
owner: devteam
revisions:
- 01e0321aca98
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfvcfintersect
owner: devteam
revisions:
- 166c4f50525f
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfbreakcreatemulti
owner: devteam
revisions:
- 9fd5d91eb91b
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfallelicprimitives
owner: devteam
revisions:
- 57a16b310fe8
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfgeno2haplo
owner: devteam
revisions:
- a3dea556218d
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcffilter
owner: devteam
revisions:
- 4bdc111b2470
- fa24bf0598f4
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcffixup
owner: devteam
revisions:
- 11f62f071125
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfgenotypes
owner: devteam
revisions:
- a60ae8af21a1
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfbedintersect
owner: devteam
revisions:
- aea8e90ad788
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfrandomsample
owner: devteam
revisions:
- 6257ee3b50d3
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfhethom
owner: devteam
revisions:
- 8254e0fe7358
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfsort
owner: devteam
revisions:
- dd44c3f416c3
- ee60203e68d9
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfprimers
owner: devteam
revisions:
- 17096387c0e6
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfcombine
owner: devteam
revisions:
- 1f0ba67cc85a
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfleftalign
owner: devteam
revisions:
- 29f9b782727e
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcf2tsv
owner: devteam
revisions:
- 285060661b45
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: vcfaddinfo
owner: devteam
revisions:
- 6ea73d6151ec
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_call
owner: iuc
revisions:
- 07396b423218
- c277260d3fab
- f0d44631365f
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_norm
owner: iuc
revisions:
- 271965b55437
- 5226c31ac6d3
- 5fa262ce95dd
- ebb2e12a6de1
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_csq
owner: iuc
revisions:
- 9f69e7d58d03
- d237eaef451f
- f01b2c9506b9
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_plugin_frameshifts
owner: iuc
revisions:
- 399b40b2bcab
- 3c6952a2b0e4
- b03c0b3e67a6
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_plugin_color_chrs
owner: iuc
revisions:
- 36960e552ddc
- 7d9166ecd10f
- 845a7025ba81
tool_panel_section_id: variant_calling
tool_panel_section_label: Variant Calling
- name: bcftools_cnv
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