Snakemake Wrappers
0.67.0

Wrappers

  • ARRIBA
  • ART
  • BAMTOOLS
  • BCFTOOLS
  • BEDTOOLS
  • BENCHMARK
  • BISMARK
  • BOWTIE2
  • BUSCO
  • BWA
  • BWA-MEM2
  • CAIROSVG
  • CLUSTALO
  • CUTADAPT
  • DEEPTOOLS
  • DEEPVARIANT
  • DELLY
  • EPIC
  • FASTP
  • FASTQ_SCREEN
  • FASTQC
  • FGBIO
  • FILTLONG
  • FREEBAYES
  • GATK
    • GATK APPLYBQSR
    • GATK BASERECALIBRATOR
    • GATK BASERECALIBRATORSPARK
    • GATK COMBINEGVCFS
    • GATK GENOTYPEGVCFS
    • GATK HAPLOTYPECALLER
    • GATK MUTECT2
    • GATK SELECTVARIANTS
    • GATK SPLITNCIGARREADS
    • GATK VARIANTFILTRATION
    • GATK VARIANTRECALIBRATOR
  • GATK3
  • GDC-API
  • GDC-CLIENT
  • GENOMEPY
  • GRIDSS
  • HAP.PY
  • HISAT2
  • HMMER
  • HOMER
  • IGV-REPORTS
  • INFERNAL
  • JANNOVAR
  • KALLISTO
  • LAST
  • LOFREQ
  • MACS2
  • 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
  • STRLING
  • TABIX
  • TRANSDECODER
  • TRIM_GALORE
  • TRIMMOMATIC
  • TRINITY
  • TXIMPORT
  • UCSC
  • UMIS
  • VARSCAN
  • VCFTOOLS
  • VEMBRANE
  • VEP

Meta-Wrappers

  • BWA_MAPPING
  • STAR-ARRIBA
Snakemake Wrappers
  • Docs »
  • GATK
  • Edit on GitHub

GATKΒΆ

For gatk, the following wrappers are available:

  • GATK APPLYBQSR
  • GATK BASERECALIBRATOR
  • GATK BASERECALIBRATORSPARK
  • GATK COMBINEGVCFS
  • GATK GENOTYPEGVCFS
  • GATK HAPLOTYPECALLER
  • GATK MUTECT2
  • GATK SELECTVARIANTS
  • GATK SPLITNCIGARREADS
  • GATK VARIANTFILTRATION
  • GATK VARIANTRECALIBRATOR
Next Previous

© Copyright 2016, The Snakemake team Revision 2ba693d6.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: 0.67.0
Versions
latest
stable
0.67.0
0.66.0
0.65.0
0.64.0
0.63.0
0.62.0
0.61.0
0.60.1
0.60.0
0.59.2
0.59.1
0.59.0
0.58.0
0.57.0
0.56.0
0.55.1
0.55.0
0.54.0
0.53.0
0.52.0
0.51.3
0.51.2
0.51.1
0.51.0
0.50.4
0.50.3
0.50.2
0.50.1
0.50.0
0.49.0
0.48.0
0.47.0
0.46.0
0.45.1
0.40.2
0.40.1
0.40.0
0.39.0
0.38.1
0.38.0
0.37.1
0.37.0
0.36.0
0.35.2
0.35.1
0.35.0
0.34.0
0.33.0
0.32.0
0.31.1
0.31.0
0.30.0
0.29.0
0.28.0
0.27.1
0.27.0
0.26.1
0.26.0
0.25.0
0.24.0
0.23.1
0.23.0
0.22.0
0.21.0
0.20.1
0.20.0
0.19.4
0.19.3
0.19.2
0.19.1
0.19.0
0.18.0
0.17.4
0.17.3
0.17.2
0.17.1
0.17.0
0.16.0
0.15.4
0.15.3
0.15.1
0.15.0
0.14.2
0.14.1
0.14.0
0.13.2
0.13.1
0.13.0
0.12.0
0.11.0
0.10.0
0.9.0
0.8.0
0.7.0
0.6.0
0.5.0
0.4.0
0.3.0
0.2.0
0.1.0
v0.0.13
0.0.13
0.0.12
0.0.11
0.0.10
0.0.9
0.0.8
0.0.7
0.0.6
0.0.5
0.0.4
0.0.3
0.0.2
0.0.1
Downloads
html
On Read the Docs
Project Home
Builds

Free document hosting provided by Read the Docs.