Nextflow Modules
Showing module(s) with keyword "gatk4"
| Module | Keywords | Description |
|---|---|---|
| nf-core/gatk4/analyzecovariates | bqsr gatk4 genomics | Evaluate and compare base quality score recalibration (BQSR) tables |
| nf-core/gatk4/annotateintervals | annotateintervals annotation bed gatk4 intervals | Annotates intervals with GC content, mappability, and segmental-duplication content |
| nf-core/gatk4/applybqsr | bam base quality score recalibration bqsr cram gatk4 | Apply base quality score recalibration (BQSR) to a bam file |
| nf-core/gatk4/applyvqsr | 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 | allele-specific asereadcounter gatk4 vcf | Calculates the allele-specific read counts for allele-specific expression analysis of RNAseq data |
| nf-core/gatk4/baserecalibrator | base quality score recalibration table bqsr gatk4 sort | Generate recalibration table for Base Quality Score Recalibration (BQSR) |
| nf-core/gatk4/bedtointervallist | bed bedtointervallist gatk4 interval list | Creates an interval list from a bed file and a reference dict |
| nf-core/gatk4/calculatecontamination | 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 | gatk4 bam cram sam calibratedragstrmodel | estimates the parameters for the DRAGstr model |
| nf-core/gatk4/cnnscorevariants | cnnscorevariants gatk4 variants | Apply a Convolutional Neural Net to filter annotated variants |
| nf-core/gatk4/collectreadcounts | collectreadcounts bam cram gatk4 | Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. |
| nf-core/gatk4/collectsvevidence | gatk4 collectsvevidence structural variants metrics | Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. |
| nf-core/gatk4/combinegvcfs | gvcf gatk4 vcf combinegvcfs short variant discovery | Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file |
| nf-core/gatk4/composestrtablefile | composestrtablefile dragstr gatk4 | This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel. |
| nf-core/gatk4/concordance | concordance gatk4 gatk genomics variant calling genotyping vcf comparison | Evaluate concordance of an input VCF against a validated truth VCF |
| nf-core/gatk4/condensedepthevidence | condensedepthevidence evidence gatk4 | Merges adjacent DepthEvidence records |
| nf-core/gatk4/createreadcountpanelofnormals | createreadcountpanelofnormals gatk4 panelofnormals | Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel. |
| nf-core/gatk4/createsequencedictionary | createsequencedictionary dictionary fasta gatk4 | Creates a sequence dictionary for a reference sequence |
| nf-core/gatk4/createsomaticpanelofnormals | createsomaticpanelofnormals gatk4 panelofnormals | Create a panel of normals constraining germline and artifactual sites for use with mutect2. |