Man pages for TearsWillFall/variantCall
An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems
| annotate_sv_type | Get SV type from svaba generated VCF |
| bgzip | Bzips a VCF file |
| call_ASEQ | Wrapper around ASEQ tool for pileup data. |
| call_bcftools_parallel | Variant calling using bcftools on parallel per genomic region |
| call_clonet | This function is a wrapper around CLONET function |
| call_fings | Filters SNVs from any variant caller to remove false... |
| call_fings_parallel | Filters SNVs from any variant caller to remove false... |
| call_HaplotypeCaller | Wrapper for GATK HaplotypeCaller for Germline Variant calling |
| call_mutect2 | Variant calling using MuTECT2 |
| call_mutect2_parallel | Variant calling using MuTECT2 on parallel per genomic region |
| call_platypus | Variant calling using Platypus |
| call_segments | Call segments for panel, exome and WGS data using CNVkit This... |
| call_sv_manta | Call Somatic/Germline structural variants using Manta This... |
| call_sv_manta_parallel | Call Somatic/Germline variants using MANTA in parallel This... |
| call_sv_svaba | Structural variant calling using svaba |
| call_sv_svaba_parallel | Structural variant calling using svaba in parallel |
| call_variants | Variant calling of Somatic and Germline (MuTECT2, Platypus... |
| call_variants_strelka | Call Somatic/Germline single nucleotide variants using... |
| call_variants_strelka_parallel | Call Somatic/Germline variants using Strelka in parallel This... |
| call_vep | Predict variant effect using VEP |
| call_vep_maf | Variant annotation in MAF format |
| check_and_unzip | Check and unzip gz compressed file |
| CNNScoreVariants | Annotate a VCF with scores from a Convolutional Neural... |
| compress_and_index_vcf | Compress and index vcf file |
| estimate_contamination | VCF contamination estimation using GATK |
| estimate_contamination_parallel | VCF contamination estimation using GATK |
| FilterVariantTranches | Filter Variant Tranches (Mutect2) |
| filter_VEP | Filter VEP results |
| fix_mnps | VCF fix MNPs |
| format_ASEQ_pileup | ASEQ pileup formatting for downstream analysis This function... |
| format_PM_data | Format vcf for downstream point mutatation analysis. |
| format_segment_data | Format segmentation data for downstream analysis using... |
| format_SNP_data | This function filter and formats heterozygous SNP data for... |
| generate_CLONET_config | This function generates a config files for CLONET pipeline |
| generate_CLONET_sample_info | This function generates a sample_info file for CLONET... |
| generate_sets | Generate a 1:n sets between a group of vcfs |
| get_pileup_summary | BAM pileup summary for known sites using GATK |
| get_sv_type | Get SV type from svaba generated VCF |
| learn_orientation | Learn Read Orientation Model (Mutect2) |
| merge_maf | This function merges a group of files in MAF format This... |
| pipe | Pipe operator |
| plot_allelic_imbalance | This function generates a plot of allelic imbalance from... |
| plot_celullarity | This function generates a plot of ploidy and celularity... |
| plot_cn_calls | This function generates a plot of ploidy and celularity... |
| plot_evolutionary_distance | This function generates a plot of reltionship between samples... |
| process_maf | This function processes a MAF file This function takes the... |
| process_variants | Process variants generated using variant_call and... |
| split_vcf | Splits multisample VCF file into multiple VCFs |
| tab_indx | Index tab separated genomic regions |
| vcf_annotate | VCF annotation using bcftools |
| vcf_bcftools | Variant calling using bcftools |
| vcf_communality | VCF communality |
| vcf_concatenate | VCF file concatenation |
| vcf_filtering | VCF filtering using GATK |
| vcf_filter_variants | VCF filtering using bcftools |
| vcf_format | VCF formating using bcftools |
| vcf_intersect_bed | Intersect vcf with bed file |
| vcf_sets | Generate a set between a group of vcfs usign bcftools |
| vcf_sort | Sort VCF file |
| vcf_stats_merge | VCF stats file concatenation |
