SAMTOOLS CALMD¶
Calculates MD and NM tags. For more information see SAMtools documentation.
URL:
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"
params:
"-E" # optional params string
threads: 2
wrapper:
"0.80.1/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==1.11
Authors¶
- Filipe G. Vieira
Code¶
__author__ = "Filipe G. Vieira"
__copyright__ = "Copyright 2020, Filipe G. Vieira"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
out_name, out_ext = path.splitext(snakemake.output[0])
out_ext = out_ext[1:].upper()
shell(
"samtools calmd --threads {snakemake.threads} {snakemake.params} --output-fmt {out_ext} {snakemake.input.aln} {snakemake.input.ref} > {snakemake.output[0]} {log}"
)