How to enable lofreq cluster command?

[jwsohn]

Hi.

Can I ask a question about installing optional commands? I tried to compile lofreq from the source package but the compiled binary does not show lowfreq cluster command. How can I enable lowfreq cluster command? The extra command of lowfreq vcfplot works fine.

$ lofreq cluster
FATAL(lofreq_main.c|main:336): Unrecognized command 'cluster'

The lofreq command line output is:

$ lofreq 

       |             ____|                 
       |       _ \   |     __|  _ \   _` | 
       |      (   |  __|  |     __/  (   | 
      _____| \___/  _|   _|   \___| \__, | 
                                        _| 

Fast and sensitive inference of SNVs and indels

Usage: lofreq <command> [options]

  Main Commands:
    call          : Call variants
    call-parallel : Call variants in parallel
    somatic       : Call somatic variants

  Preprocessing Commands
    viterbi       : Viterbi realignment
    indelqual     : Insert indel qualities
    alnqual       : Insert base and indel alignment qualities

  Other Commands:
    checkref      : Check that reference fasta and BAM file match
    filter        : Filter variants in VCF file
    uniq          : Test whether variants predicted in only one sample really are unique
    plpsummary    : Print pileup summary per position
    vcfset        : VCF set operations
    version       : Print version info

  Samtools Clones:
    faidx         : Create index for fasta file
    index         : Create index for BAM file
    idxstats      : Print stats for indexed BAM file

  Extra Tools (if installed):
    vcfplot       : Plot VCF statistics

I tried both the GitHub source and lofreq_star-2.1.5.tar.gz source package. PyVCF, Scipy, Numpy, and Matplotlib are all installed.

Thanks,

Jung-woo

[andreas-wilm]

Dear Jung-woo,

the cluster command is considered experimental, which is why we never included it in the main set of tools. You can however find the script called lofreq2_cluster.py in src/tools/scripts/ of the source package or here on Github. It requires James Casbon's pyvcf.

Hope this help, Andreas