PINDEL¶
Call variants with pindel.
Software dependencies¶
- pindel ==0.2.5b8
Example¶
This wrapper can be used in the following way:
pindel_types = ["D", "BP", "INV", "TD", "LI", "SI", "RP"]
rule pindel:
input:
ref="genome.fasta",
# samples to call
samples=["mapped/a.bam"],
# bam configuration file, see http://gmt.genome.wustl.edu/packages/pindel/quick-start.html
config="pindel_config.txt"
output:
expand("pindel/all_{type}", type=pindel_types)
params:
# prefix must be consistent with output files
prefix="pindel/all",
extra="" # optional parameters (except -i, -f, -o)
log:
"logs/pindel.log"
threads: 4
wrapper:
"0.61.0/bio/pindel/call"
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.
Authors¶
- Johannes Köster
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import os
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
shell(
"pindel -T {snakemake.threads} {snakemake.params.extra} -i {snakemake.input.config} "
"-f {snakemake.input.ref} -o {snakemake.params.prefix} {log}"
)