GT-COMPREADS-REFCO(1)

NAME
gt-compreads-refcompress - Generates compact encoding for fastq data using Reference Compressed Reads (RCR).

SYNOPSIS

gt compreads refcompress [option ...] (-bam file -ref file)

OPTIONS

-v
    be verbose (default: no)

-mquals
    store mapping quality for each read (default: no)

-quals
    store all quality values for each read, this implies enabling of option "vquals" (default: no)

-vquals
    store quality values of read positions having variations compared to reference (default: no)

-descs
    store read name for each read (default: no)

-ureads
    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
    Index file (generated by the gt encseq tool) for reference genome. (default: undefined)

-bam
    File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)

-name
    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

AUTHOR

Report bugs to <gt-users@genometools.org>.