Nextflow Modules
Showing module(s) with keyword "sentieon"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/sentieon/applyvarcal | Process | sentieon applyvarcal varcal VQSR | Apply a score cutoff to filter variants based on a recalibration table. Sentieon's Aplyvarcal 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 previous step VarCal and a target sensitivity value. https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm |
| nf-core/sentieon/bwaindex | Process | index fasta genome reference sentieon | Create BWA index for reference genome |
| nf-core/sentieon/bwamem | Process | mem bwa alignment map fastq bam sentieon | Performs the alignment of fastq files to a fasta reference using Sentieon's BWA MEM |
| nf-core/sentieon/collectvcmetrics | Process | vcf sentieon genomics | Accelerated implementation of the Picard CollectVariantCallingMetrics tool. |
| nf-core/sentieon/coveragemetrics | Process | coverage sentieon genomics | Accelerated implementation of the GATK DepthOfCoverage tool. |
| nf-core/sentieon/datametrics | Process | metrics bam sentieon | Collects multiple quality metrics from a bam file |
| nf-core/sentieon/dedup | Process | mem dedup map bam cram sentieon | Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which, in turn, marks or removes duplicate reads. |
| nf-core/sentieon/dnamodelapply | Process | dnamodelapply vcf filter sentieon | modifies the input VCF file by adding the MLrejected FILTER to variants that are rejected by the selected machine learning model |
| nf-core/sentieon/dnascope | Process | dnascope sentieon variant_calling | DNAscope algorithm performs an improved version of Haplotype variant calling. |
| nf-core/sentieon/haplotyper | Process | sentieon haplotypecaller haplotype | Runs Sentieon's haplotyper for germline variant calling. |
| nf-core/sentieon/hsmetrics | Process | metrics bam sentieon | Collects hybrid-selection (HS) metrics for a SAM or BAM file. |
| nf-core/sentieon/qualcal | Process | base quality score recalibration bqsr sentieon | Generate recalibration table and optionally perform base quality recalibration |
| nf-core/sentieon/readwriter | Process | merge convert readwriter sentieon | Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file. |
| nf-core/sentieon/rsemcalculateexpression | Process | rsem expression quantification sentieon | Calculate expression with RSEM |
| nf-core/sentieon/rsempreparereference | Process | rsem genome index sentieon | Prepare a reference genome for RSEM |
| nf-core/sentieon/tnfilter | Process | tnfilter filter sentieon tnhaplotyper2 vcf | Filters the raw output of sentieon/tnhaplotyper2. |
| nf-core/sentieon/tnhaplotyper2 | Process | tnseq tnhaplotyper2 sentieon variant_calling | Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs. |
| nf-core/sentieon/tnscope | Process | tnscope sentieon variant_calling | TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm. |
| nf-core/sentieon/varcal | Process | sentieon varcal variant recalibration | Module for Sentieons VarCal. The VarCal algorithm calculates the Variant Quality Score Recalibration (VQSR). VarCal builds a recalibration model for scoring variant quality. https://support.sentieon.com/manual/usages/general/#varcal-algorithm |