GATK GET PILEUP SUMMARIES¶
Summarizes counts of reads that support reference, alternate and other alleles
URL: https://gatk.broadinstitute.org/hc/en-us/articles/360037593451-GetPileupSummaries
Example¶
This wrapper can be used in the following way:
rule test_gatk_get_pileup_summaries:
input:
bam="mapped/a.bam",
intervals="genome/intervals.bed",
variants="genome/variants.vcf.gz",
output:
"summaries.table",
threads: 1
resources:
mem_mb=1024,
params:
extra="",
log:
"logs/summary.log",
wrapper:
"v1.19.1/bio/gatk/getpileupsummaries"
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¶
gatk4=4.3.0.0
snakemake-wrapper-utils=0.5.0
Input/Output¶
Input:
bam
: Path to bam file (sorted and indexed)intervals
: Path to one or more BED genomic intervals over which to operatevariants
: Path to a VCF containing allele frequencies (pbgzipped and tabix indexed)
Output:
- Path to output table
Params¶
extra
: Optional parameters
Authors¶
Code¶
#!/usr/bin/env python3
# coding: utf-8
"""Snakemake wrapper for GATK GetPileupSummaries"""
__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2022, Thibault Dayris"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
with tempfile.TemporaryDirectory() as tempdir:
shell(
"gatk GetPileupSummaries "
"--java-options '{java_opts}' "
"--input {snakemake.input.bam} "
"--intervals {snakemake.input.intervals} "
"--variant {snakemake.input.variants} "
"--output {snakemake.output[0]} "
"--tmp-dir {tempdir} "
"{extra} "
"{log} "
)