VARLOCIRAPTOR ESTIMATE ALIGNMENT PROPERTIES

Estimate alignment properties for variant calling with varlociraptor

URL: https://varlociraptor.github.io/docs/estimating/

Example

This wrapper can be used in the following way:

rule varlociraptor_alignment_properties:
    input:
        ref="resources/genome.fasta",
        alignments=["results/alignments/{sample}.bam"],
        ref_idx="resources/genome.fasta.fai",
        aln_idx=["results/alignments/{sample}.bam.bai"],
    output:
        "results/alignment-properties/{sample}.json",
    log:
        "logs/varlociraptor/alignment-properties/{sample}.log",
    params:
        extra="",  # optional additional parameters
    wrapper:
        "v5.5.2-17-g33d5b76/bio/varlociraptor/estimate-alignment-properties"

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

varlociraptor=8.6.0

Input/Output

Input:

reference genome
read alignments (may be multiple bams)

Output:

varlociraptor alignment properties

Authors

Johannes Köster

Code

import subprocess as sp

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

sp.run(
    "varlociraptor estimate alignment-properties "
    f"{snakemake.params.get('extra', '')} {snakemake.input.ref} "
    f"--bams {snakemake.input.alignments} "
    f"> {snakemake.output[0]} {log}",
    check=True,
    shell=True,
)