gt-compreads-refcompress1
Generates compact encoding for fastq data using reference compressed reads (rcr).
Usage
gt compreads
refcompress
[option ...]
(-bam
file
-ref
file)
Overview
-
-v [yes|no] -
be verbose (default: no)
-
-mquals [yes|no] -
store mapping quality for each read (default: no)
-
-quals [yes|no] -
store all quality values for each read, this implies enabling of option "vquals" (default: no)
-
-vquals [yes|no] -
store quality values of read positions having variations compared to reference (default: no)
-
-descs [yes|no] -
store read name for each read (default: no)
-
-ureads [yes|no] -
store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " _unmapped.fastq" (default: no)
-
-ref [string] -
Index file (generated by the gt encseq tool) for reference genome. (default: undefined)
-
-bam [string] -
File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)
-
-name [string] -
specify base name for RCR to be generated. If not set, base name will be set to base name of value given for option "bam" (default: undefined)
-
-help -
display help and exit
-
-version -
display version information and exit
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.