VARSCAN2 - SNPEFF
This meta-wrapper includes the following steps:
Example
This meta-wrapper can be used by integrating the following into your workflow:
rule get_genome_fasta:
output:
"genome.fasta",
threads: 1
log:
"logs/get_genome_fasta.log",
params:
species="saccharomyces_cerevisiae",
datatype="dna",
build="R64-1-1",
release="105",
wrapper:
"v5.8.3/bio/reference/ensembl-sequence"
rule samtools_mpileup:
input:
bam=expand(
"{sample}.sorted.bam",
sample=("a", "b"),
),
reference_genome="genome.fasta",
output:
"samtools/mpileup.gz",
threads: 1
log:
"logs/samtools_mpileup.log",
params:
extra=" --count-orphans ",
wrapper:
"v5.8.3/bio/samtools/mpileup"
rule varscan2_somatic:
input:
mpileup="samtools/mpileup.gz",
output:
snp="varscan2/snp.vcf",
indel="varscan2/indel.vcf",
threads: 1
log:
"logs/varscan2_somatic.log",
params:
extra=" --strand-filter 1 ",
wrapper:
"v5.8.3/bio/varscan/somatic"
rule snpeff_download:
output:
directory("resources/snpeff/R64-1-1.105"),
threads: 1
log:
"logs/snpeff_download.log",
params:
reference="R64-1-1.105",
wrapper:
"v5.8.3/bio/snpeff/download"
rule snpeff_annotate:
input:
calls="varscan2/snp.vcf",
db="resources/snpeff/R64-1-1.105",
output:
calls="snpeff/annotated.vcf",
stats="snpeff/annotated.html",
csvstats="snpeff/annotated.csv",
threads: 1
log:
"logs/snpeff_annotate.log",
params:
extra=" -nodownload -noLog ",
wrapper:
"v5.8.3/bio/snpeff/annotate"
Note that input, output and log file paths can be chosen freely, as long as the dependencies between the rules remain as listed here. For additional parameters in each individual wrapper, please refer to their corresponding documentation (see links below).
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Used wrappers
The following individual wrappers are used in this meta-wrapper:
Please refer to each wrapper in above list for additional configuration parameters and information about the executed code.