SAMTOOLS CALMD

Calculates MD and NM tags.

URL: http://www.htslib.org/doc/samtools-calmd.html

Example

This wrapper can be used in the following way:

rule samtools_calmd:
    input:
        aln="{sample}.bam",  # Can be 'sam', 'bam', or 'cram'
        ref="genome.fasta",
    output:
        "{sample}.calmd.bam",
    log:
        "{sample}.calmd.log",
    params:
        extra="-E",  # optional params string
    threads: 2
    wrapper:
        "v5.3.0-16-g710597c/bio/samtools/calmd"

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

• samtools=1.21

• snakemake-wrapper-utils=0.6.2

Input/Output

Input:

• SAM/BAM/CRAM file

Output:

• SAM/BAM/CRAM file

• SAM/BAM/CRAM index file (optional)

Params

• extra: additional program arguments (not -@/–threads, –write-index, -m, -o or -O/–output-fmt).

Authors

• Filipe G. Vieira

Code

__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2020, Filipe G. Vieira"
__license__ = "MIT"


from snakemake.shell import shell
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=False, stderr=True)

shell(
    "samtools calmd {samtools_opts} {extra} {snakemake.input.aln} {snakemake.input.ref} > {snakemake.output[0]} {log}"
)