4.41. isnvs_one_sample

Intrahost variant calling with V-Phaser2. Requires an assembled genome and a BAM of aligned reads against that same genome.

4.41.1. Inputs

4.41.1.1. Required inputs

isnvs_one_sample.isnvs_per_sample.assembly_fasta
File — Default: None
???

isnvs_one_sample.isnvs_per_sample.mapped_bam
File — Default: None
???

4.41.1.2. Other inputs

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isnvs_one_sample.isnvs_per_sample.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???

isnvs_one_sample.isnvs_per_sample.machine_mem_gb
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.maxBias
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.minReadsPerStrand
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.removeDoublyMappedReads
Boolean — Default: true
???

isnvs_one_sample.isnvs_per_sample.sample_name
String — Default: basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")
???

isnvs_one_sample.isnvs_per_sample.threads
Int? — Default: None
???

4.41.2. Outputs

isnvs_one_sample.isnvs_viral_phylo_version
String
???

isnvs_one_sample.isnvsFile
File
???

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