Nextflow Modules
Showing module(s) with keyword "metrics"
| Module | Keywords | Description |
|---|---|---|
| nf-core/bamreadcount | BAM CRAM metrics genomics | bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. |
| nf-core/bcftools/pluginimputeinfo | impute-info bcftools imputation metrics tags vcf | Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. |
| 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/picard/collectalignmentsummarymetrics | metrics alignment statistics bam | Collect metrics about the alignment summary of a paired-end library. |
| nf-core/picard/collecthsmetrics | alignment metrics statistics insert hybrid-selection quality bam | Collects hybrid-selection (HS) metrics for a SAM or BAM file. |
| nf-core/picard/collectinsertsizemetrics | metrics alignment insert statistics bam | Collect metrics about the insert size distribution of a paired-end library. |
| nf-core/picard/collectmultiplemetrics | alignment metrics statistics insert quality bam | Collect multiple metrics from a BAM file |
| nf-core/picard/collectrnaseqmetrics | rna bam metrics alignment statistics quality | Collect metrics from a RNAseq BAM file |
| nf-core/picard/collectvariantcallingmetrics | vcf metrics variant calling statistics | Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file |
| nf-core/picard/collectwgsmetrics | alignment metrics statistics quality bam | Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. |
| nf-core/picard/crosscheckfingerprints | alignment metrics statistics fingerprint bam | Checks that all data in the set of input files appear to come from the same individual |
| nf-core/picard/meanqualitybycycle | metrics alignment mean statistics bam | Collect metrics about the mean quality by cycle of a paired-end library. |
| nf-core/sentieon/datametrics | metrics bam sentieon | Collects multiple quality metrics from a bam file |
| nf-core/sentieon/hsmetrics | metrics bam sentieon | Collects hybrid-selection (HS) metrics for a SAM or BAM file. |
| nf-core/sentieon/wgsmetrics | metrics bam sentieon | Collects whole genome quality metrics from a bam file |