Repository revision
16:021693fdadaa

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

bcftools norm tool metadata
Miscellaneous
Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows
bcftools_norm
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10
1.10
bcftools 2>&1 | grep 'Version:'
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.10 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.4.0.0
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.3.1.0
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.3.1
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.3.0
bcftools_norm
Requirements (dependencies defined in the <requirements> tag set)
name version type
bcftools 1.10 package
htslib 1.10 package
samtools 1.10 package
gawk 5.0.1 package
Functional tests
name inputs outputs required files
Test-1 input_file: norm.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
normalize_indels: True
output_type: v
name: value
norm.vcf
norm.fa
value
Test-2 input_file: norm.vcf
reference_source|fasta_ref: norm
reference_source|reference_source_selector: cached
normalize_indels: True
output_type: v
name: value
norm.vcf
value
Test-3 input_file: norm.split.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
multiallelics|mode: -
output_type: v
name: value
norm.split.vcf
norm.fa
value
Test-4 input_file: norm.split.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
normalize_indels: True
multiallelics|mode: -
output_type: v
name: value
norm.split.vcf
norm.fa
value
Test-5 input_file: norm.merge.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
multiallelics|mode: +
output_type: v
name: value
norm.merge.vcf
norm.fa
value
Test-6 input_file: norm.merge.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
multiallelics|strict_filter: True
multiallelics|mode: +
output_type: v
name: value
norm.merge.vcf
norm.fa
value
Test-7 input_file: norm.setref.vcf
reference_source|fasta_ref: norm.fa
reference_source|reference_source_selector: history
check_ref: ws
output_type: v
name: value
norm.setref.vcf
norm.fa
value