BCFTOOLS MERGE¶
Merge vcf/bcf files with bcftools.
URL: http://www.htslib.org/doc/bcftools.html#merge
Example¶
This wrapper can be used in the following way:
rule bcftools_merge:
input:
calls=["a.bcf", "b.bcf"],
output:
"all.bcf",
log:
"all.log"
params:
uncompressed_bcf=False,
extra="", # optional parameters for bcftools concat (except -o)
wrapper:
"v1.31.1/bio/bcftools/merge"
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, -o/–output, or -O/–output-type).
Software dependencies¶
bcftools=1.17
snakemake-wrapper-utils=0.5.3
Authors¶
- Patrik Smeds
- Filipe G. Vieira
Code¶
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@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_ref=False, parse_memory=False)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell("bcftools merge {bcftools_opts} {extra} {snakemake.input} {log}")