Files in msubirana/ergWgsTools

What the Package Does (One Line, Title Case)

R/amber.R R/annovarAnnotation.R R/bamCoverage.R R/bamReadCountsToDf.R R/bamTofastqPicard.R R/bcftoolsReheader.R R/bwaAlignment.R R/cobalt.R R/facets.R R/filterPass.R R/gridss.R R/hisat2R.R R/manta.R R/mantaStrelka2Calling.R R/mergeStrelka.R R/merge_pass_strelka.R R/mosdepth.R R/mutect2Calling.R R/mutect2_gatk3_8.R R/oncodriveclustl.R R/oncodrivefml.R R/postCalling.R R/purple.R R/purple_full.R R/realignBamBwa.R R/reheaderBam.R R/renameSampleBam.R R/somaticWgsAnalysis.R R/strelka2.R R/variantAnnotation.R R/variantCalling.R R/wgsSomaticAnalysis.R README.md man/annovarAnnotation.Rd man/bamCoverage.Rd man/bamTofastqPicard.Rd man/bcftoolsReheader.Rd man/bwaAlignment.Rd man/facets.Rd man/filterPass.Rd man/fpfilterTool.Rd man/hisat2R.Rd man/insertSizePindel.Rd man/manta.Rd man/mantaCalling.Rd man/mosdepth.Rd man/museCalling.Rd man/mutect2Calling.Rd man/oncodriveclustl.Rd man/oncodrivefml.Rd man/pindelCalling.Rd man/postCalling.Rd man/radiaCalling.Rd man/realignBamBwa.Rd man/reheaderBam.Rd man/renameSampleBam.Rd man/sambambaIndex.Rd man/samtoolsIndex.Rd man/somaticWgsAnalysis.Rd man/somaticsniperCalling.Rd man/strelka.Rd man/strelka2Calling.Rd man/variantAnnotation.Rd man/variantCalling.Rd man/varscan2Calling.Rd man/wgsSomaticPreprocessing.Rd onGoing/wgsSomaticCalling.R test.R tmp/annovarAnnotation.R tmp/annovarAnnotation_strelka.R tmp/bamCoverage.R tmp/bamCoverage_sge.R tmp/bamReadCountsToDf.R tmp/bamTofastqPicard.R tmp/bamTofastqPicard_sge.R tmp/bamTofastqPicardbwaAlignment.R tmp/bamTofastqPicardbwaAlignment_sge.R tmp/boxplot.R tmp/bwaAlignment.R tmp/bwaAlignment_sge.R tmp/facets.R tmp/facets_host.R tmp/fastqc.R tmp/fastqc_sge.R tmp/filterPass_manta.R tmp/filterPass_strelka.R tmp/fq_bam_mutect_manta_strelka.R tmp/fq_bam_mutect_manta_strelka_host.R tmp/fq_bam_mutect_manta_strelka_sge.R tmp/genomicDataCommons.R tmp/hisat2R.R tmp/hisat2R_sge.R tmp/mafTools.R tmp/mafTools_sge.R tmp/merge_pass_strelka_host.R tmp/mosdepth.R tmp/mosdepth_host.R tmp/mosdepth_sge.R tmp/museCalling.R tmp/mutect2Calling.R tmp/mutect2Calling_sge.R tmp/mutect2_gatk3_8.R tmp/mutect2_gatk3_8_host.R tmp/mutect2_gatk3_8_host_parallel.R tmp/mutect2_gatk3_8_sge.R tmp/oncodriveclustl.R tmp/oncodriveclustl_modeling_sge.R tmp/oncodriveclustl_sge.R tmp/oncodrivefml.R tmp/oncodrivefml_sge.R tmp/pindelCalling.R tmp/plot_vcf_parameters.R tmp/postCalling.R tmp/postCalling_sge.R tmp/post_calling.R tmp/purple_full.R tmp/purple_full_host.R tmp/purple_full_sge.R tmp/rToSge_alignFastqBwa.R tmp/rToSge_strelka2Calling_all_samples.R tmp/radiaCalling.R tmp/reheaderBam.R tmp/reheaderBam_sge.R tmp/rename_files_and_reheader.R tmp/rename_files_and_reheader_icgc.R tmp/rename_vcfs_strelka.R tmp/rtoSge.R tmp/samtoolsIndex.R tmp/samtoolsIndex_sge.R tmp/samtoolsSort.R tmp/somaticsniperCalling.R tmp/strelka2Calling.R tmp/strelka2Calling_all_samples.R tmp/strelka2Calling_sge.R tmp/tmp_gridss.R tmp/tmp_variantCalling.R tmp/variables.R tmp/variantAnnotation.R tmp/varscan2Calling.R tmp/wgsSomaticPreprocessing.R toFinish/gridss-purple-linx.R toFinish/gridss.R