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

[xmy1990]

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 : #74

Thanks

[joshfactorial]

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

[xmy1990]

@#123 (comment)
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]

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]

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