Nextflow Modules
Showing module(s) with keyword "gatk4"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bam_applybqsr | Workflow | bam cram bqsr recalibration gatk4 | Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed. |
| nf-core/bam_create_som_pon_gatk | Workflow | gatk4 mutect2 genomicsdbimport createsomaticpanelofnormals variant_calling genomicsdb_workspace panel_of_normals | Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals. |
| nf-core/bam_tumor_normal_somatic_variant_calling_gatk | Workflow | gatk4 mutect2 learnreadorientationmodel getpileupsummaries calculatecontamination filtermutectcalls variant_calling tumor_only filtered_vcf | Perform variant calling on a paired tumor normal set of samples using mutect2 tumor normal mode. f1r2 output of mutect2 is run through learnreadorientationmodel to get the artifact priors. Run the input bam files through getpileupsummarries and then calculatecontamination to get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls, artifact priors and the contamination & segmentation tables for additional filtering. |
| nf-core/bam_tumor_only_somatic_variant_calling_gatk | Workflow | gatk4 mutect2 getpileupsummaries calculatecontamination filtermutectcalls variant_calling tumor_only filtered_vcf | Perform variant calling on a single tumor sample using mutect2 tumor only mode. Run the input bam file through getpileupsummarries and then calculatecontaminationto get the contamination and segmentation tables. Filter the mutect2 output vcf using filtermutectcalls and the contamination & segmentation tables for additional filtering. |
| nf-core/gatk4/analyzecovariates | Process | bqsr gatk4 genomics | Evaluate and compare base quality score recalibration (BQSR) tables |
| nf-core/gatk4/annotateintervals | Process | annotateintervals annotation bed gatk4 intervals | Annotates intervals with GC content, mappability, and segmental-duplication content |
| nf-core/gatk4/applybqsr | Process | bam base quality score recalibration bqsr cram gatk4 | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4/applyvqsr | Process | gatk4 variant quality score recalibration vcf vqsr | Apply a score cutoff to filter variants based on a recalibration table. AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR). Specifically, it applies filtering to the input variants based on the recalibration table produced in the first step by VariantRecalibrator and a target sensitivity value. |
| nf-core/gatk4/asereadcounter | Process | allele-specific asereadcounter gatk4 vcf | Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data |
| nf-core/gatk4/baserecalibrator | Process | base quality score recalibration table bqsr gatk4 sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/gatk4/bedtointervallist | Process | bed bedtointervallist gatk4 interval list | Creates an interval list from a bed file and a reference dict |
| nf-core/gatk4/calculatecontamination | Process | gatk4 calculatecontamination cross-samplecontamination getpileupsummaries filtermutectcalls | Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls. |
| nf-core/gatk4/calibratedragstrmodel | Process | gatk4 bam cram sam calibratedragstrmodel | estimates the parameters for the DRAGstr model |
| nf-core/gatk4/cnnscorevariants | Process | cnnscorevariants gatk4 variants | Apply a Convolutional Neural Net to filter annotated variants |
| nf-core/gatk4/collectreadcounts | Process | collectreadcounts bam cram gatk4 | Collects read counts |