BCFTOOLS CONCAT
Concatenate vcf/bcf files with bcftools.
URL: http://www.htslib.org/doc/bcftools.html#concat
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:
"v5.8.0/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.
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, or -O/–output-type).
Software dependencies
bcftools=1.21
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
vcf files
Output:
Concatenated VCF/BCF file
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__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 concat {bcftools_opts} {extra} {snakemake.input.calls} {log}")