FREEBAYES¶
Call small genomic variants with freebayes.
Software dependencies¶
- freebayes ==1.1.0
- bcftools ==1.5
Example¶
This wrapper can be used in the following way:
rule freebayes:
input:
ref="genome.fasta",
# you can have a list of samples here
samples="mapped/{sample}.bam"
output:
"calls/{sample}.vcf" # either .vcf or .bcf
log:
"logs/freebayes/{sample}.log"
params:
"" # optional parameters
wrapper:
"0.17.4/bio/freebayes"
Note that input, output and log file paths can be chosen freely. When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2017, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
pipe = ""
if snakemake.output[0].endswith(".bcf"):
pipe = "| bcftools view -Ob -"
shell("(freebayes {snakemake.params} -f {snakemake.input.ref} "
" {snakemake.input.samples} {pipe} > {snakemake.output[0]}) {log}")