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version: 1.2 | ||
workflows: | ||
- name: 'COVID-19-CONSENSUS-CONSTRUCTION' | ||
primaryDescriptorPath: /consensus-from-variation.ga | ||
subclass: Galaxy | ||
testParameterFiles: | ||
- /consensus-from-variation-test.yml |
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0.1 | ||
--------- | ||
- Initial version of COVID-19: consensus construction |
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COVID-19: consensus construction | ||
-------------------------------- | ||
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This workflow aims at generating reliable consensus sequences from variant | ||
calls according to transparent criteria that capture at least some of the | ||
complexity of variant calling. | ||
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It takes a collection of VCFs and a collection of the corresponding | ||
aligned reads (for the purpose of calculating genome-wide coverage) such as | ||
produced by any of the four variant calling workflows in | ||
https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling | ||
and generates a collection of viral consensus sequences and a multisample FASTA | ||
of all these sequences. | ||
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Each consensus sequence is guaranteed to capture all called, filter-passing | ||
variants as defined in the VCF of its sample that reach a user-defined | ||
consensus allele frequency threshold. | ||
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Filter-failing variants and variants below a second user-defined minimal | ||
allele frequency threshold will be ignored. | ||
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Genomic positions of filter-passing variants with an allele frequency in | ||
between the two thresholds will be hard-masked (with N) in the consensus | ||
sequence of their sample. | ||
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Genomic positions with a coverage (calculated from the read alignments input) | ||
below another user-defined threshold will be hard-masked, too, unless they are | ||
consensus variant sites. |
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- doc: Test consensus building from called variants | ||
job: | ||
Reference genome: | ||
class: File | ||
location: 'https://zenodo.org/record/4555735/files/NC_045512.2_reference.fasta?download=1' | ||
aligned reads data for depth calculation: | ||
class: Collection | ||
collection_type: 'list' | ||
elements: | ||
- identifier: SRR11578257 | ||
class: File | ||
path: test-data/aligned_reads_for_coverage.bam | ||
Variant calls: | ||
class: Collection | ||
collection_type: 'list' | ||
elements: | ||
- identifier: SRR11578257 | ||
class: File | ||
path: test-data/final_snpeff_annotated_variants.vcf | ||
outputs: | ||
multisample_consensus_fasta: | ||
file: test-data/masked_consensus.fa | ||
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