GATK HAPLOTYPECALLER

Run gatk HaplotypeCaller.

URL: https://gatk.broadinstitute.org/hc/en-us/articles/9570334998171-HaplotypeCaller

Example

This wrapper can be used in the following way:

rule haplotype_caller:
    input:
        # single or list of bam files
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
        # known="dbsnp.vcf"  # optional
    output:
        vcf="calls/{sample}.vcf",
    #       bam="{sample}.assemb_haplo.bam",
    log:
        "logs/gatk/haplotypecaller/{sample}.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    threads: 4
    resources:
        mem_mb=1024,
    wrapper:
        "v4.6.0/bio/gatk/haplotypecaller"

rule haplotype_caller_gvcf:
    input:
        # single or list of bam files
        bam="mapped/{sample}.bam",
        ref="genome.fasta",
        # known="dbsnp.vcf"  # optional
    output:
        gvcf="calls/{sample}.g.vcf",
    #       bam="{sample}.assemb_haplo.bam",
    log:
        "logs/gatk/haplotypecaller/{sample}.log",
    params:
        extra="",  # optional
        java_opts="",  # optional
    threads: 4
    resources:
        mem_mb=1024,
    wrapper:
        "v4.6.0/bio/gatk/haplotypecaller"

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 java_opts param allows for additional arguments to be passed to the java compiler, e.g. -XX:ParallelGCThreads=10 (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).

• The extra param allows for additional program arguments.

Software dependencies

• gatk4=4.5.0.0

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• BAM file

Output:

• GVCF file

Authors

• Johannes Köster

• Jake VanCampen

• Filipe G. Vieira

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2018, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"


import os
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

bams = snakemake.input.bam
if isinstance(bams, str):
    bams = [bams]
bams = list(map("--input {}".format, bams))

intervals = snakemake.input.get("intervals", "")
if not intervals:
    intervals = snakemake.params.get("intervals", "")
if intervals:
    intervals = "--intervals {}".format(intervals)

known = snakemake.input.get("known", "")
if known:
    known = "--dbsnp " + str(known)

vcf_output = snakemake.output.get("vcf", "")
if vcf_output:
    output = " --output " + str(vcf_output)

gvcf_output = snakemake.output.get("gvcf", "")
if gvcf_output:
    output = " --emit-ref-confidence GVCF " + " --output " + str(gvcf_output)

if (vcf_output and gvcf_output) or (not gvcf_output and not vcf_output):
    if vcf_output and gvcf_output:
        raise ValueError(
            "please set vcf or gvcf as output, not both! It's not supported by gatk"
        )
    else:
        raise ValueError("please set one of vcf or gvcf as output (not both)!")

bam_output = snakemake.output.get("bam", "")
if bam_output:
    bam_output = " --bam-output " + str(bam_output)

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "gatk --java-options '{java_opts}' HaplotypeCaller"
        " --native-pair-hmm-threads {snakemake.threads}"
        " {bams}"
        " --reference {snakemake.input.ref}"
        " {intervals}"
        " {known}"
        " {extra}"
        " --tmp-dir {tmpdir}"
        " {output}"
        " {bam_output}"
        " {log}"
    )