picard_bam_fastq: Title
In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr
Description
Title
Usage
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picard_bam_fastq(bam, samplename = opts_flow$get("samplename"),
paired = TRUE, split = FALSE, num_reads = 8e+06,
split_fq_exe = system.file("scripts/split_fq", package = "ngsflows"),
java_exe = opts_flow$get("java_exe"),
java_mem = opts_flow$get("java_mem"),
java_tmp = opts_flow$get("java_tmp"),
picard_dir = opts_flow$get("picard_dir"),
bam_fastq_opts = "INCLUDE_NON_PF_READS=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false RE_REVERSE=true VALIDATION_STRINGENCY=LENIENT")
Arguments
picard_dir
flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.
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Description
Title
Usage
1 2 3 4 5 6 7 8 | picard_bam_fastq(bam, samplename = opts_flow$get("samplename"),
paired = TRUE, split = FALSE, num_reads = 8e+06,
split_fq_exe = system.file("scripts/split_fq", package = "ngsflows"),
java_exe = opts_flow$get("java_exe"),
java_mem = opts_flow$get("java_mem"),
java_tmp = opts_flow$get("java_tmp"),
picard_dir = opts_flow$get("picard_dir"),
bam_fastq_opts = "INCLUDE_NON_PF_READS=true INCLUDE_NON_PRIMARY_ALIGNMENTS=false RE_REVERSE=true VALIDATION_STRINGENCY=LENIENT")
|
Arguments
picard_dir |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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