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VCF header is incorrect for genotype probabilities #51

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cjw85 opened this issue Oct 7, 2020 · 2 comments
Closed

VCF header is incorrect for genotype probabilities #51

cjw85 opened this issue Oct 7, 2020 · 2 comments

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@cjw85
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cjw85 commented Oct 7, 2020

The artic pipeline uses longshot after medaka to produce some ancilliary statistics of SARS-CoV-2 variants. The header associated with some probabilities incorrectly specifies some numbers as integer when in fact they are written as floats in teh records of the file, see nanoporetech/medaka#213

From src/print_output.rs:

let headerstr3 = format!("##INFO=<ID=PH,Number=G,Type=Integer,Description=\"PHRED-scaled Probabilities of Phased Genotypes\">
@phspo
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phspo commented Oct 7, 2020

@cjw85 thanks for forwarding this to the correct place ;)

@vibansal
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Fixed in new release v0.4.2. Thanks.

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