Files in TearsWillFall/variantCall

An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

R/analysis.R R/util.R R/utils-pipe.R man/CNNScoreVariants.Rd man/FilterVariantTranches.Rd man/annotate_sv_type.Rd man/bgzip.Rd man/call_ASEQ.Rd man/call_HaplotypeCaller.Rd man/call_bcftools_parallel.Rd man/call_clonet.Rd man/call_fings.Rd man/call_fings_parallel.Rd man/call_mutect2.Rd man/call_mutect2_parallel.Rd man/call_platypus.Rd man/call_segments.Rd man/call_sv_manta.Rd man/call_sv_manta_parallel.Rd man/call_sv_svaba.Rd man/call_sv_svaba_parallel.Rd man/call_variants.Rd man/call_variants_strelka.Rd man/call_variants_strelka_parallel.Rd man/call_vep.Rd man/call_vep_maf.Rd man/check_and_unzip.Rd man/compress_and_index_vcf.Rd man/estimate_contamination.Rd man/estimate_contamination_parallel.Rd man/filter_VEP.Rd man/fix_mnps.Rd man/format_ASEQ_pileup.Rd man/format_PM_data.Rd man/format_SNP_data.Rd man/format_segment_data.Rd man/generate_CLONET_config.Rd man/generate_CLONET_sample_info.Rd man/generate_sets.Rd man/get_pileup_summary.Rd man/get_sv_type.Rd man/learn_orientation.Rd man/merge_maf.Rd man/pipe.Rd man/plot_allelic_imbalance.Rd man/plot_celullarity.Rd man/plot_cn_calls.Rd man/plot_evolutionary_distance.Rd man/process_maf.Rd man/process_variants.Rd man/split_vcf.Rd man/tab_indx.Rd man/vcf_annotate.Rd man/vcf_bcftools.Rd man/vcf_communality.Rd man/vcf_concatenate.Rd man/vcf_filter_variants.Rd man/vcf_filtering.Rd man/vcf_format.Rd man/vcf_intersect_bed.Rd man/vcf_sets.Rd man/vcf_sort.Rd man/vcf_stats_merge.Rd