Snakemake Wrappers
0.61.0

Wrappers

  • ARRIBA
  • ART
  • BAMTOOLS
  • BCFTOOLS
  • BEDTOOLS
  • BISMARK
  • BOWTIE2
  • BUSCO
  • BWA
  • CAIROSVG
  • CLUSTALO
  • CUTADAPT
  • DEEPVARIANT
  • DELLY
  • EPIC
  • FASTP
  • FASTQ_SCREEN
  • FASTQC
  • FGBIO
  • FILTLONG
  • FREEBAYES
  • GATK
    • GATK BASERECALIBRATOR
    • GATK COMBINEGVCFS
    • GATK GENOTYPEGVCFS
    • GATK HAPLOTYPECALLER
    • GATK MUTECT2
    • GATK SELECTVARIANTS
    • GATK SPLITNCIGARREADS
    • GATK VARIANTFILTRATION
    • GATK VARIANTRECALIBRATOR
  • GATK3
  • GDC-API
  • GDC-CLIENT
  • HAP.PY
  • HISAT2
  • HMMER
  • HOMER
  • IGV-REPORTS
  • INFERNAL
  • JANNOVAR
  • KALLISTO
  • LAST
  • LOFREQ
  • MINIMAP2
  • MSISENSOR
  • MULTIQC
  • NANOSIM-H
  • NGS-DISAMBIGUATE
  • OPTITYPE
  • PALADIN
  • PEAR
  • PICARD
  • PINDEL
  • PLASS
  • PRESEQ
  • PRIMERCLIP
  • PROSOLO
  • PTRIMMER
  • PYFASTAQ
  • RAZERS3
  • REFERENCE
  • REFGENIE
  • RUBIC
  • SALMON
  • SAMBAMBA
  • SAMTOOLS
  • SEQTK
  • SHOVILL
  • SICKLE
  • SNP-MUTATOR
  • SNPEFF
  • SNPSIFT
  • SOURMASH
  • SRA-TOOLS
  • STAR
  • STRELKA
  • TABIX
  • TRANSDECODER
  • TRIM_GALORE
  • TRIMMOMATIC
  • TRINITY
  • TXIMPORT
  • UCSC
  • UMIS
  • VARSCAN
  • VCFTOOLS
  • VEP
Snakemake Wrappers
  • Docs »
  • GATK
  • Edit on GitHub

GATKΒΆ

For gatk, the following wrappers are available:

  • GATK BASERECALIBRATOR
  • GATK COMBINEGVCFS
  • GATK GENOTYPEGVCFS
  • GATK HAPLOTYPECALLER
  • GATK MUTECT2
  • GATK SELECTVARIANTS
  • GATK SPLITNCIGARREADS
  • GATK VARIANTFILTRATION
  • GATK VARIANTRECALIBRATOR
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