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}.bcf",
output:
"{prefix}.norm.vcf",
log:
"{prefix}.norm.log",
params:
extra="--rm-dup none", # optional
wrapper:
"v1.1.0/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
snakemake-wrapper-utils=0.2
Authors¶
- Dayne Filer
- Filipe G. Vieira
Code¶
__author__ = "Dayne Filer"
__copyright__ = "Copyright 2019, Dayne Filer"
__email__ = "dayne.filer@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
bcftools_opts = get_bcftools_opts(snakemake, parse_memory=False, parse_temp_dir=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"bcftools norm {bcftools_opts} {extra} {snakemake.input[0]} -o {snakemake.output[0]} {log}"
)