SAMTOOLS FIXMATE

Use samtools to correct mate information after BWA mapping.

Example

This wrapper can be used in the following way:

rule samtools_fixmate:
    input:
        "mapped/{input}",
    output:
        "fixed/{input}",
    log:
        "{input}.log",
    message:
        "Fixing mate information in {wildcards.input}"
    threads: 1
    params:
        extra="",
    wrapper:
        "v4.6.0-24-g250dd3e/bio/samtools/fixmate/"

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 extra param allows for additional program arguments (not -@/–threads or -O/–output-fmt).

• For more information see, http://www.htslib.org/doc/samtools-fixmate.html

Software dependencies

• samtools=1.21

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• bam or sam file (.bam,.sam)

Output:

• bam or sam file (.bam,.sam)

Authors

• Thibault Dayris

• Filipe G. Vieira

Code

"""Snakemake wrapper for samtools fixmate"""

__author__ = "Thibault Dayris"
__copyright__ = "Copyright 2019, Dayris Thibault"
__email__ = "thibault.dayris@gustaveroussy.fr"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake.utils import makedirs
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(
    snakemake, parse_write_index=False, parse_output=False
)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "samtools fixmate {samtools_opts} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
)