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fix: use latest varlociraptor release and ignore all biases in case of known lineage variant calling #575

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Nov 8, 2022
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2 changes: 1 addition & 1 deletion workflow/envs/varlociraptor.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ channels:
- bioconda
- nodefaults
dependencies:
- varlociraptor =4.9
- varlociraptor =5.3
10 changes: 10 additions & 0 deletions workflow/rules/common.smk
Original file line number Diff line number Diff line change
Expand Up @@ -805,6 +805,16 @@ def get_list_of_amplicon_states_assembler(samples):


def get_varlociraptor_bias_flags(wildcards):
if wildcards.varrange == "lineage-variants":
# Known variants, we don't want to use bias detection at all.
# Rationale: the determined biases are hints for artifacts, which are particularly
# important to maintain a high precision with denovo calls. When there is prior knowledge
# about a variant like here, they are too conservative. E.g., when I see a typical omicron
# variant in a sample, I tend to believe it even if it happens to have a strand bias.
return (
"--omit-strand-bias --omit-read-orientation-bias --omit-read-position-bias "
"--omit-softclip-bias --omit-homopolymer-artifact-detection --omit-alt-locus-bias"
)
if is_amplicon_data(wildcards.sample):
# no bias detection possible
return (
Expand Down