BCFTOOLS VIEW¶
View vcf/bcf file in a different format.
URL:
Example¶
This wrapper can be used in the following way:
rule bcf_view_sample_file:
input:
"{prefix}.bcf", # input bcf/vcf needs to be first input
index="{prefix}.bcf.csi", # other inputs are optional
samples="samples.txt",
output:
"{prefix}.view_sample.vcf",
log:
"log/{prefix}.view_sample.vcf.log",
params:
# optional extra parameters
extra=lambda w, input: f"-S {input.samples}",
wrapper:
"0.85.0/bio/bcftools/view"
rule bcf_view_o_vcf:
input:
"{prefix}.bcf",
output:
"{prefix}.view.vcf",
log:
"log/{prefix}.view.vcf.log",
params:
extra="",
wrapper:
"0.85.0/bio/bcftools/view"
rule bcf_view_o_vcf_gz:
input:
"{prefix}.bcf",
output:
"{prefix}.view.vcf.gz",
log:
"log/{prefix}.view.vcf.gz.log",
params:
extra="",
wrapper:
"0.85.0/bio/bcftools/view"
rule bcf_view_o_bcf:
input:
"{prefix}.bcf",
output:
"{prefix}.view.bcf",
log:
"log/{prefix}.view.bcf.log",
params:
extra="",
wrapper:
"0.85.0/bio/bcftools/view"
rule bcf_view_o_uncompressed_bcf:
input:
"{prefix}.bcf",
output:
"{prefix}.view.uncompressed.bcf",
log:
"log/{prefix}.view.uncompressed.bcf.log",
params:
uncompressed_bcf=True,
extra="",
wrapper:
"0.85.0/bio/bcftools/view"
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
Notes¶
- The uncompressed_bcf param allows to specify that a BCF output should be uncompressed (ignored otherwise).
- The bcftools_use_mem param controls whether to pass the resources.mem_mb to bcftools
- The extra param allows 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
- Nikos Tsardakas Renhuldt
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)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"bcftools view {bcftools_opts} "
"{extra} "
"{snakemake.input[0]} "
"-o {snakemake.output} "
"{log}"
)