75 lines
2.7 KiB
JSON
75 lines
2.7 KiB
JSON
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{
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// 使用 IntelliSense 了解相关属性。
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// 悬停以查看现有属性的描述。
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// 欲了解更多信息，请访问: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"type": "java",
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"name": "BaseRecalibrator",
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"request": "launch",
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// "mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
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"mainClass": "org.broadinstitute.gatk.engine.ProtectedCLGATK",
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"projectName": "gatk-tools-protected",
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//"classPaths": [
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// "${workspaceFolder}/target/excutable/GenomeAnalysisTK.jar",
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// "${workspaceFolder}/target/excutable/lib/*"
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//],
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//"classPaths": [
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// "${workspaceFolder}/protected/gatk-tools-protected/target/classes/",
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// "${workspaceFolder}/public/gatk-engine/target/classes/",
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//],
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//"vmArgs": "-verbose:class",
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"args": [
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"-T", "BaseRecalibrator",
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"-R",
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"~/reference/bwa/human_g1k_v37_decoy.fasta",
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"-knownSites",
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"~/data/reference/hg19/vcfs/dbsnp_138.b37.vcf",
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"-knownSites",
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"~/data/reference/hg19/vcfs/1000G_phase1.indels.b37.vcf",
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"-I",
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//"~/data/fastdup-mini-md.bam",
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//"~/data/f1kw.sam",
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//"~/data/ft1kw.sam",
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//"~/data/difft1kw.sam",
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//"~/data/diff.sam",
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//"~/data/diff2kw.sam",
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//"~/data1/x.bam",
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//"~/data1/y.bam",
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"~/data/z.bam",
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//"~/data/z-3.sam",
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//"~/data/z-1.sam",
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"-o",
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// "./output/out-bqsr.table",
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//"./output/x.table",
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//"./output/y.table",
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//"./output/z.table",
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//"./output/z-3.table",
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"./output/f-1.table",
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// "--enable-baq",
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]
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},
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{
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"type": "java",
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"name": "ApplyBQSR",
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"request": "launch",
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"mainClass": "org.broadinstitute.gatk.engine.CommandLineGATK",
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"projectName": "gatk",
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"args": [
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"ApplyBQSR",
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"-R",
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"~/reference/bwa/human_g1k_v37_decoy.fasta",
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"-I",
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"~/data1/x.bam",
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//"~/data/z.bam",
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//"~/data/ft1kw.sam",
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"-bqsr",
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"./output/f-1.table",
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"-O",
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"./output/f-1.sam",
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]
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}
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]
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}
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