Miscellaneous |
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
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 |