BCFTOOLS CONCAT¶
Concatenate vcf/bcf files with bcftools. For more information see BCFtools documentation.
URL:
Example¶
This wrapper can be used in the following way:
rule bcftools_concat:
input:
calls=["a.bcf", "b.bcf"],
output:
"all.bcf",
log:
"logs/all.log",
params:
uncompressed_bcf=False,
extra="", # optional parameters for bcftools concat (except -o)
threads: 4
resources:
mem_mb=10,
wrapper:
"0.85.0/bio/bcftools/concat"
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=1.12
snakemake-wrapper-utils==0.2.0
Notes¶
- The uncompressed_bcf param allows to specify that a BCF output should be uncompressed (ignored otherwise).
- The extra param alllows for additional program arguments (not –threads, `-O/–output-type, -m/–max-mem, or -T/–temp-dir).
- For more information see, https://samtools.github.io/bcftools/bcftools.html
Authors¶
- Johannes Köster
- Filipe G. Vieira
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
bcftools_opts = get_bcftools_opts(snakemake, parse_memory=False)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"bcftools concat {snakemake.params.extra} {bcftools_opts} -o {snakemake.output[0]} "
"{snakemake.input.calls} "
"{log}"
)