Repository revision
5:7dfca164d2e3

Repository 'lofreq_filter'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter

Lofreq filter tool metadata
Miscellaneous
called variants posteriorly
lofreq_filter
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
2.1.5+galaxy0
lofreq version | grep version | cut -d ' ' -f 2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.4+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.3.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.3.1
lofreq_filter
Requirements (dependencies defined in the <requirements> tag set)
name version type
lofreq 2.1.5 package
Additional information about this tool
## filter variants with lofreq 
        lofreq filter -i $invcf --no-defaults --verbose
        $flag_or_drop
        ${filter_by_type.keep_only}
        #if str($filter_by_type.keep_only) in ['', '--only-snvs']:
            #if str($filter_by_type.qual.snvqual_filter.snvqual) == 'min-phred':
                -Q ${filter_by_type.qual.snvqual_filter.snvqual_thresh}
            #elif str($filter_by_type.qual.snvqual_filter.snvqual) == 'mtc':
                -q ${filter_by_type.qual.snvqual_filter.snvqual_mtc}
                -r ${filter_by_type.qual.snvqual_filter.snvqual_alpha}
                -s ${filter_by_type.qual.snvqual_filter.snvqual_ntests}
            #end if
        #end if
        #if str($filter_by_type.keep_only) in ['', '--only-indels']:
            #if str($filter_by_type.qual.indelqual_filter.indelqual) == 'min-phred':
                -K ${filter_by_type.qual.indelqual_filter.indelqual_thresh}
            #elif str($filter_by_type.qual.indelqual_filter.indelqual) == 'mtc':
                -k ${filter_by_type.qual.indelqual_filter.indelqual_mtc}
                -l ${filter_by_type.qual.indelqual_filter.indelqual_alpha}
                -m ${filter_by_type.qual.indelqual_filter.indelqual_ntests}
            #end if
        #end if
        -v ${coverage.cov_min}
        -V ${coverage.cov_max}
        -a ${af.af_min}
        -A ${af.af_max}
        #if str($sb.sb_filter.strand_bias) == 'max-phred':
            -B ${sb.sb_filter.sb_thresh}
        #elif str($sb.sb_filter.strand_bias) == 'mtc':
            -b ${sb.sb_filter.sb_mtc}
            -c ${sb.sb_filter.sb_alpha}
        #end if
        #if str($sb.sb_filter.strand_bias) != 'no':
            ${sb.sb_filter.sb_compound}
            ${sb.sb_filter.sb_indels}
        #end if
        -o filtered.vcf
    
None
False
Functional tests
name inputs outputs required files
Test-1 invcf: call-out2.vcf
filter_by_type|qual|snvqual_filter|snvqual_thresh: 38
filter_by_type|qual|snvqual_filter|snvqual: min-phred
filter_by_type|qual|indelqual_filter|indelqual_thresh: 20
filter_by_type|qual|indelqual_filter|indelqual: min-phred
name: value
call-out2.vcf
value
Test-2 invcf: call-out2.vcf
filter_by_type|qual|snvqual_filter|snvqual_alpha: 0.01
filter_by_type|qual|snvqual_filter|snvqual_mtc: bonf
filter_by_type|qual|snvqual_filter|snvqual_ntests: 66
filter_by_type|qual|snvqual_filter|snvqual: mtc
filter_by_type|keep_only: --only-snvs
name: value
call-out2.vcf
value
Test-3 invcf: call-out2.vcf
filter_by_type|qual|snvqual_filter|snvqual_thresh: 38
filter_by_type|qual|snvqual_filter|snvqual: min-phred
filter_by_type|qual|indelqual_filter|indelqual_thresh: 20
filter_by_type|qual|indelqual_filter|indelqual: min-phred
flag_or_drop: --print-all
name: value
call-out2.vcf
value