1 variants skipped: (qual filtered / ref genotypes / invalid syntax)

ncsa / NEAT

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

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1 variants skipped: (qual filtered / ref genotypes / invalid syntax) #123

Open xmy1990 opened 1 month ago

xmy1990 commented 1 month ago

hi, I want to insert 4 indels use neat v3.0 and get the follow log, found 3 valid variants in input vcf.

1 variants skipped: (qual filtered / ref genotypes / invalid syntax)
0 variants skipped due to multiple variants found per position

the skipped variant had a 0/0 genotype, the other 3 variants all had a 1/1 genotype.

genotype is the reason for being skipped?

I found the same issue : https://github.com/ncsa/NEAT/issues/74

Thanks

joshfactorial commented 1 month ago

Right, NEAT will skip variants with a 0/0 genotype, as there is nowhere to insert it.

xmy1990 commented 1 month ago

@https://github.com/ncsa/NEAT/issues/123#issuecomment-2231527538 Thank you so much! I still have three issues:

I'm a beginner and I don't quite understand why there's no place to insert 0/0.
Could you explain in simple terms what the software requires for genotypes?
If I don't input a genotype, will it randomly assign one?

joshfactorial commented 1 month ago

A 0/0 genotype indicates both alleles matched the reference. Basically, it's saying the variant isn't actually present in specimen. For a heterozygous variant, it would be either 1/0 or 0/1, or for homozygous, you'd have 1/1. To save some processing time, NEAT will ignore 0/0 variants up front and throw them out. So long as at least one allele has the variant (a '1' somewhere) then it will take it.

Yes, NEAT will generate a random genotype if it doesn't find one.

xmy1990 commented 1 month ago

Thank you very much for the detailed response. I understand now.