| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp/2.4.2.a (this tool) |
| toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp/2.3.6.a |
| varscan_mpileup2snp |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| varscan | 2.4.2 | package |
| Additional information about this tool |
varscan mpileup2snp
'${mpileup_input}'
#if $extended_parameters.parameters == "extended"
--min-coverage $extended_parameters.varscan_min_coverage
--min-reads2 $extended_parameters.varscan_min_reads2
--min-avg-qual $extended_parameters.varscan_min_avg_qual
--min-var-freq $extended_parameters.varscan_min_var_freq
--min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
--p-value $extended_parameters.varscan_p_value
$extended_parameters.varscan_strand_filter
$extended_parameters.varscan_variants
#end if
#if $varscan_output == "vcf" or $varscan_output.value == "vcf"
--output-vcf 1
#end if
> '${snv_output}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
extended_parameters|parameters: default mpileup_input: hg19_mutant.mpileup |
snv_output: hg19_mutant.vcf |
hg19_mutant.mpileup hg19_mutant.vcf |
| Test-2 |
extended_parameters|varscan_min_avg_qual: 15 extended_parameters|varscan_min_freq_for_hom: 0.75 extended_parameters|varscan_min_var_freq: 0.01 extended_parameters|varscan_min_reads2: 2 extended_parameters|varscan_variants: False extended_parameters|parameters: extended mpileup_input: hg19_mutant.mpileup extended_parameters|varscan_strand_filter: True extended_parameters|varscan_min_coverage: 8 extended_parameters|varscan_p_value: 0.99 |
snv_output: hg19_mutant.2.vcf |
hg19_mutant.mpileup hg19_mutant.2.vcf |