SAMTOOLS BAM2FQ SEPARATE¶
Convert a bam file with paired end reads back to unaligned reads in a two separate fastq files with samtools. Reads that are not properly paired are discarded (READ_OTHER and singleton reads in samtools bam2fq documentation), as are secondary (0x100) and supplementary reads (0x800).
URL:
Example¶
This wrapper can be used in the following way:
rule samtools_bam2fq_separate:
input:
"mapped/{sample}.bam"
output:
"reads/{sample}.1.fq",
"reads/{sample}.2.fq"
params:
sort = "-m 4G",
bam2fq = "-n"
threads: # Remember, this is the number of samtools' additional threads
3 # At least 2 threads have to be requested on cluster sumbission.
# Thus, this value - 2 will be sent to samtools sort -@ argument.
wrapper:
"0.80.1/bio/samtools/bam2fq/separate"
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
Notes¶
- Samtools -@/–threads takes one integer as input. This is the number of additional threads and not raw threads.
Authors¶
- David Laehnemann
- Victoria Sack
Code¶
__author__ = "David Laehnemann, Victoria Sack"
__copyright__ = "Copyright 2018, David Laehnemann, Victoria Sack"
__email__ = "david.laehnemann@hhu.de"
__license__ = "MIT"
import os
from snakemake.shell import shell
params_sort = snakemake.params.get("sort", "")
params_bam2fq = snakemake.params.get("bam2fq", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
prefix = os.path.splitext(snakemake.output[0])[0]
# Samtools takes additional threads through its option -@
# One thread is used bu Samtools sort
# One thread is used by Samtools bam2fq
# So snakemake.threads has to take them into account
# before allowing additional threads through samtools sort -@
threads = "" if snakemake.threads <= 2 else " -@ {} ".format(snakemake.threads - 2)
shell(
"(samtools sort -n "
" {threads} "
" -T {prefix} "
" {params_sort} "
" {snakemake.input[0]} | "
"samtools bam2fq "
" {params_bam2fq} "
" -1 {snakemake.output[0]} "
" -2 {snakemake.output[1]} "
" -0 /dev/null "
" -s /dev/null "
" -F 0x900 "
" - "
") {log}"
)