gatk3 gatk3 printreads

gatk3 printreads

Version:
3.8
Identifier: TL_6ad060_49.80
Tool
1__author__ = "Patrik Smeds"
2__copyright__ = "Copyright 2019, Patrik Smeds"
3__email__ = "patrik.smeds@gmail.com.com"
4__license__ = "MIT"
5
6import os
7
8from snakemake.shell import shell
9from snakemake_wrapper_utils.java import get_java_opts
10
11extra = snakemake.params.get("extra", "")
12java_opts = get_java_opts(snakemake)
13
14input_bam = snakemake.input.bam
15input_recal_data = snakemake.input.recal_data
16input_ref = snakemake.input.ref
17
18log = snakemake.log_fmt_shell(stdout=True, stderr=True)
19
20shell(
21    "gatk3 {java_opts} -T PrintReads"
22    " {extra}"
23    " -I {input_bam}"
24    " -R {input_ref}"
25    " -BQSR {input_recal_data}"
26    " -o {snakemake.output}"
27    " {log}"
28)
29