BCFTOOLS NORM¶
Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. For more information see BCFtools documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule norm_vcf:
input:
"{prefix}.vcf"
output:
"{prefix}.vcf"
params:
"" # optional parameters for bcftools norm (except -o)
wrapper:
"0.80.1/bio/bcftools/norm"
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.
Software dependencies¶
bcftools=1.11
Authors¶
- Dayne Filer
Code¶
__author__ = "Dayne Filer"
__copyright__ = "Copyright 2019, Dayne Filer"
__email__ = "dayne.filer@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
shell(
"bcftools norm {snakemake.params} {snakemake.input[0]} " "-o {snakemake.output[0]}"
)