├── .gitignore ├── CommandLineHowTo ├── deploy-script.rb ├── getweb.sh ├── interval-gene.awk ├── intervals.txt ├── random.bed ├── sample.sh.rtxt ├── sort-bed-ucsc.rb ├── tabsub.rb └── tabsub.txt ├── DiseaseGenomeMain ├── 010_download-ucsc.sh ├── 020_concatinate.sh ├── 030_download-dra.sh ├── 040_run-sra-fastq-dump.sh ├── 050_run-bwa-mem.sh ├── 060_run-samtools-sort-index.sh ├── 070_run-markduplicates.sh ├── 080_download-gatk-bundles.sh ├── 090_prep-reference-index.sh ├── 100_run-BaseRecalibrator.sh ├── 110_run-ApplyBQSR.sh ├── 120_run-HaplotypeCaller.sh ├── 130_run-GenotypeGVCFs.sh ├── 140_run-SelectVariants.sh ├── 150_run-VariantFiltration.sh ├── 160_MergeVcfs.sh ├── 210_prep-annovar-dbs.sh ├── 220_download-ToMMo.sh ├── 230_convert_35KJPNv2-snv.sh ├── 240_convert_35KJPNv2-indel.sh ├── 250_run-compileAnnovarIndex.sh ├── 310_run-table-annovar.sh ├── 320_run-awk-prioritize.sh └── Scripts │ ├── awk010_ToMMo35KJPNv2.awk │ ├── awk020_TrancateVariants.awk │ ├── awk030_NonsynonymousVariants.awk │ ├── awk040_Homozygous.awk │ ├── awk050_Heterozygous.awk │ ├── compileAnnovarIndex.pl │ ├── sort-bed.rb │ └── tommo_separate_alternatives.rb ├── DiseaseGenomeValidation ├── 010_download-ucsc.sh ├── 020_concatinate.sh ├── 030_download-dra.sh ├── 040_run-sra-fastq-dump.sh ├── 050_run-bwa-mem.sh ├── 060_run-samtools-sort-index.sh ├── 070_run-markduplicates.sh ├── 080_download-gatk-bundles.sh ├── 090_prep-reference-index.sh ├── 100_run-BaseRecalibrator.sh ├── 110_run-ApplyBQSR.sh ├── 120_run-HaplotypeCaller.sh ├── 130_run-GenotypeGVCFs.sh ├── 140_run-SelectVariants.sh ├── 150_run-VariantFiltration.sh ├── 160_MergeVcfs.sh ├── 210_prep-annovar-dbs.sh ├── 220_download-ToMMo.sh ├── 230_convert_35KJPNv2-snv.sh ├── 240_convert_35KJPNv2-indel.sh ├── 250_run-compileAnnovarIndex.sh ├── 310_run-table-annovar.sh ├── 320_run-awk-prioritize.sh ├── 330_SRY-coverage.sh ├── 340_check-earwax-snp.sh └── Scripts │ ├── awk010_ToMMo35KJPNv2.awk │ ├── awk020_TrancateVariants.awk │ ├── awk030_NonsynonymousVariants.awk │ ├── awk040_Homozygous.awk │ ├── awk050_Heterozygous.awk │ ├── compileAnnovarIndex.pl │ ├── sort-bed.rb │ └── tommo_separate_alternatives.rb ├── LICENSE └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/.gitignore -------------------------------------------------------------------------------- /CommandLineHowTo/deploy-script.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/deploy-script.rb -------------------------------------------------------------------------------- /CommandLineHowTo/getweb.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/getweb.sh -------------------------------------------------------------------------------- /CommandLineHowTo/interval-gene.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/interval-gene.awk -------------------------------------------------------------------------------- /CommandLineHowTo/intervals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/intervals.txt -------------------------------------------------------------------------------- /CommandLineHowTo/random.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/random.bed -------------------------------------------------------------------------------- /CommandLineHowTo/sample.sh.rtxt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/sample.sh.rtxt -------------------------------------------------------------------------------- /CommandLineHowTo/sort-bed-ucsc.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/sort-bed-ucsc.rb -------------------------------------------------------------------------------- /CommandLineHowTo/tabsub.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/tabsub.rb -------------------------------------------------------------------------------- /CommandLineHowTo/tabsub.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/CommandLineHowTo/tabsub.txt -------------------------------------------------------------------------------- /DiseaseGenomeMain/010_download-ucsc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/010_download-ucsc.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/020_concatinate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/020_concatinate.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/030_download-dra.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/030_download-dra.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/040_run-sra-fastq-dump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/040_run-sra-fastq-dump.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/050_run-bwa-mem.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/050_run-bwa-mem.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/060_run-samtools-sort-index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/060_run-samtools-sort-index.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/070_run-markduplicates.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/070_run-markduplicates.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/080_download-gatk-bundles.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/080_download-gatk-bundles.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/090_prep-reference-index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/090_prep-reference-index.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/100_run-BaseRecalibrator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/100_run-BaseRecalibrator.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/110_run-ApplyBQSR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/110_run-ApplyBQSR.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/120_run-HaplotypeCaller.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/120_run-HaplotypeCaller.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/130_run-GenotypeGVCFs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/130_run-GenotypeGVCFs.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/140_run-SelectVariants.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/140_run-SelectVariants.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/150_run-VariantFiltration.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/150_run-VariantFiltration.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/160_MergeVcfs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/160_MergeVcfs.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/210_prep-annovar-dbs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/210_prep-annovar-dbs.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/220_download-ToMMo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/220_download-ToMMo.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/230_convert_35KJPNv2-snv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/230_convert_35KJPNv2-snv.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/240_convert_35KJPNv2-indel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/240_convert_35KJPNv2-indel.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/250_run-compileAnnovarIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/250_run-compileAnnovarIndex.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/310_run-table-annovar.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/310_run-table-annovar.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/320_run-awk-prioritize.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/320_run-awk-prioritize.sh -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/awk010_ToMMo35KJPNv2.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/awk010_ToMMo35KJPNv2.awk -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/awk020_TrancateVariants.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/awk020_TrancateVariants.awk -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/awk030_NonsynonymousVariants.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/awk030_NonsynonymousVariants.awk -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/awk040_Homozygous.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/awk040_Homozygous.awk -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/awk050_Heterozygous.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/awk050_Heterozygous.awk -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/compileAnnovarIndex.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/compileAnnovarIndex.pl -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/sort-bed.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/sort-bed.rb -------------------------------------------------------------------------------- /DiseaseGenomeMain/Scripts/tommo_separate_alternatives.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeMain/Scripts/tommo_separate_alternatives.rb -------------------------------------------------------------------------------- /DiseaseGenomeValidation/010_download-ucsc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/010_download-ucsc.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/020_concatinate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/020_concatinate.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/030_download-dra.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/030_download-dra.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/040_run-sra-fastq-dump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/040_run-sra-fastq-dump.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/050_run-bwa-mem.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/050_run-bwa-mem.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/060_run-samtools-sort-index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/060_run-samtools-sort-index.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/070_run-markduplicates.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/070_run-markduplicates.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/080_download-gatk-bundles.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/080_download-gatk-bundles.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/090_prep-reference-index.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/090_prep-reference-index.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/100_run-BaseRecalibrator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/100_run-BaseRecalibrator.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/110_run-ApplyBQSR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/110_run-ApplyBQSR.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/120_run-HaplotypeCaller.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/120_run-HaplotypeCaller.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/130_run-GenotypeGVCFs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/130_run-GenotypeGVCFs.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/140_run-SelectVariants.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/140_run-SelectVariants.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/150_run-VariantFiltration.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/150_run-VariantFiltration.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/160_MergeVcfs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/160_MergeVcfs.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/210_prep-annovar-dbs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/210_prep-annovar-dbs.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/220_download-ToMMo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/220_download-ToMMo.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/230_convert_35KJPNv2-snv.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/230_convert_35KJPNv2-snv.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/240_convert_35KJPNv2-indel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/240_convert_35KJPNv2-indel.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/250_run-compileAnnovarIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/250_run-compileAnnovarIndex.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/310_run-table-annovar.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/310_run-table-annovar.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/320_run-awk-prioritize.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/320_run-awk-prioritize.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/330_SRY-coverage.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/330_SRY-coverage.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/340_check-earwax-snp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/340_check-earwax-snp.sh -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/awk010_ToMMo35KJPNv2.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/awk010_ToMMo35KJPNv2.awk -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/awk020_TrancateVariants.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/awk020_TrancateVariants.awk -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/awk030_NonsynonymousVariants.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/awk030_NonsynonymousVariants.awk -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/awk040_Homozygous.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/awk040_Homozygous.awk -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/awk050_Heterozygous.awk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/awk050_Heterozygous.awk -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/compileAnnovarIndex.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/compileAnnovarIndex.pl -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/sort-bed.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/sort-bed.rb -------------------------------------------------------------------------------- /DiseaseGenomeValidation/Scripts/tommo_separate_alternatives.rb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/DiseaseGenomeValidation/Scripts/tommo_separate_alternatives.rb -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/misshie/ngsdat2/HEAD/README.md --------------------------------------------------------------------------------