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.

URL: http://www.htslib.org/doc/bcftools.html#norm

Example

This wrapper can be used in the following way:

rule norm_vcf:
    input:
        "{prefix}.bcf",
        #ref="genome.fasta"  # optional reference (will be translated into the -f option)
    output:
        "{prefix}.norm.vcf",  # can also be .bcf, corresponding --output-type parameter is inferred automatically
    log:
        "{prefix}.norm.log",
    params:
        extra="--rm-dup none",  # optional
        #uncompressed_bcf=False,
    wrapper:
        "v3.9.0/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.

Notes

• The uncompressed_bcf param allows to specify that a BCF output should be uncompressed (ignored otherwise).

• The extra param allows for additional program arguments (not –threads, -f/–fasta-ref, -o/–output, or -O/–output-type).

Software dependencies

• bcftools=1.20

• snakemake-wrapper-utils=0.6.2

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)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


shell("bcftools norm {bcftools_opts} {extra} {snakemake.input[0]} {log}")