Open
Description
openedon Feb 6, 2024
Description of feature
local:
- add_info_to_vcf
- build_intervals
- create_intervals_bed
nf-core:
- ascat
- bcftools/annotate
- bcftools/concat
- bcftools/mpileup
- bcftools/sort
- bcftools/stats
- bwa/index
- bwa/mem
- bwamem2/index
- bwamem2/mem
- cat/cat
- cat/fastq
- cnvkit/antitarget
- cnvkit/batch
- cnvkit/genemetrics
- cnvkit/reference
- controlfreec/assesssignificance
- controlfreec/freec
- controlfreec/freec2bed
- controlfreec/freec2circos
- controlfreec/makegraph
- custom/dumpsoftwareversions
- deepvariant
- dragmap/align
- dragmap/hashtable
- ensemblvep/download
- ensemblvep/vep
- fastp
- fastqc
- fgbio/callmolecularconsensusreads
- fgbio/fastqtobam
- fgbio/groupreadsbyumi
- freebayes
- gatk4/applybqsr
- gatk4/applyvqsr
- gatk4/baserecalibrator
- gatk4/calculatecontamination
- gatk4/cnnscorevariants
- gatk4/createsequencedictionary
- gatk4/estimatelibrarycomplexity
- gatk4/filtermutectcalls
- gatk4/filtervarianttranches
- gatk4/gatherbqsrreports
- gatk4/gatherpileupsummaries
- gatk4/genomicsdbimport
- gatk4/genotypegvcfs
- gatk4/getpileupsummaries
- gatk4/haplotypecaller
- gatk4/intervallisttobed
- gatk4/learnreadorientationmodel
- gatk4/markduplicates
- gatk4/mergemutectstats
- gatk4/mergevcfs
- gatk4/mutect2
- gatk4/variantrecalibrator
- gatk4spark/applybqsr
- gatk4spark/baserecalibrator
- gatk4spark/markduplicates
- manta/germline
- manta/somatic
- manta/tumoronly
- mosdepth
- msisensorpro/msisomatic
- msisensorpro/scan
- multiqc
- ngscheckmate/ncm
- samblaster
- samtools/bam2fq
- samtools/collatefastq
- samtools/convert
- samtools/faidx
- samtools/index
- samtools/merge
- samtools/mpileup
- samtools/stats
- samtools/view
- sentieon/applyvarcal
- sentieon/bwamem
- sentieon/dedup
- sentieon/dnamodelapply
- sentieon/dnascope
- sentieon/gvcftyper
- sentieon/haplotyper
- sentieon/varcal
- snpeff/download
- snpeff/snpeff
- strelka/germline
- strelka/somatic
- svdb/merge
- tabix/bgziptabix
- tabix/tabix
- tiddit/sv
- untar
- unzip
- vcftools
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