BCFTOOLS MPILEUP
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files.
URL: http://www.htslib.org/doc/bcftools.html#mpileup
Example
This wrapper can be used in the following way:
rule bcftools_mpileup:
input:
alignments=["mapped/{sample}.bam", "mapped/{sample}.bam"],
ref="genome.fasta", # this can be left out if --no-reference is in options
index="genome.fasta.fai",
output:
pileup="pileups/{sample}.pileup.bcf",
params:
uncompressed_bcf=False,
extra="--max-depth 100 --min-BQ 15",
log:
"logs/bcftools_mpileup/{sample}.log",
wrapper:
"v5.8.0-3-g915ba34/bio/bcftools/mpileup"
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=1.21
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
alignments
: SAM/BAM/CRAM file(s)ref
: reference genomereference genome index
Output:
pileup file
Params
uncompressed_bcf
: uncompressed BCF (ignored otherwise)extra
: additional program arguments
Code
__author__ = "Michael Hall"
__copyright__ = "Copyright 2020, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.bcftools import get_bcftools_opts
extra = snakemake.params.get("extra", "")
bcftools_opts = get_bcftools_opts(
snakemake, parse_ref=("--no-reference" not in extra), parse_memory=False
)
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
class MissingReferenceError(Exception):
pass
shell("bcftools mpileup {bcftools_opts} {extra} {snakemake.input.alignments} {log}")