BCFTOOLS REHEADER¶
Change header or sample names of vcf/bcf file.
URL: http://www.htslib.org/doc/bcftools.html#reheader
Example¶
This wrapper can be used in the following way:
rule bcftools_reheader:
input:
vcf="a.bcf",
## new header, can be omitted if "samples" is set
header="header.txt",
## file containing new sample names, can be omitted if "header" is set
samples="samples.tsv",
output:
"a.reheader.bcf",
log:
"reheader.log",
params:
uncompressed_bcf=False,
extra="", # optional parameters for bcftools reheader
view_extra="", # optional parameters for bcftools view
threads: 2
wrapper:
"v1.15.2/bio/bcftools/reheader"
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, -O/–output-type, or -T/–temp-prefix).
Software dependencies¶
bcftools=1.14
snakemake-wrapper-utils=0.4
Authors¶
- Jan Forster
- Filipe G. Vieira
Code¶
__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"
import tempfile
from pathlib import Path
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", "")
view_extra = snakemake.params.get("view_extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
## Extract arguments
header = snakemake.input.get("header", "")
if header:
header = f"-h {header}"
samples = snakemake.input.get("samples", "")
if samples:
samples = f"-s {samples}"
with tempfile.TemporaryDirectory() as tmpdir:
tmp_prefix = Path(tmpdir) / "bcftools_reheader."
shell(
"(bcftools reheader"
" --threads {snakemake.threads}"
" {header}"
" {samples}"
" {extra}"
" --temp-prefix {tmp_prefix}"
" {snakemake.input[0]}"
"| bcftools view"
" {bcftools_opts}"
" {view_extra}"
") {log}"
)