SAMTOOLS IDXSTATS¶
Use samtools to retrieve and print stats form indexed bam, sam or cram files. For more information see SAMtools documentation.
URL:
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:
"0.80.0/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}")