SAMTOOLS IDXSTATS¶
Use samtools to retrieve and print stats form indexed bam, sam or cram files. For more information see SAMtools documentation.
Example¶
This wrapper can be used in the following way:
rule samtools_idxstats:
input:
bam="mapped/{sample}.bam",
idx="mapped/{sample}.bam.bai"
output:
"mapped/{sample}.bam.idxstats"
log:
"logs/samtools/idxstats/{sample}.log"
wrapper:
"0.74.0/bio/samtools/idxstats"
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==1.10
Input/Output¶
Input:
- indexed sam, bam or cram file (.sam, .bam, .cram)
- corresponding index files
Output:
- idxstat file (.idxstats)
Authors¶
- Antonie Vietor
Code¶
__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell("samtools idxstats {snakemake.input.bam} > {snakemake.output[0]} {log}")