Hannes Pétur Eggertsson

Hi, thanks. I can see it seems odd that FILTER=PASS when no genotype call has PASS. I will add a check for this in the future. I don't know if...

Hello, I would suggest keeping them, and also use the genotype PHRED genotype likelihood field (PL) in the VCF (if your association pipeline supports it). Best, Hannes

Thanks for reporting. Could you provide me a reference and the input VCF around the variant so I can reproduce the problem? The variants must be in the svimmer output...

I am able to reproduce the problem, thanks for reporting. Hopefully I can push a fix for it soon. Best, Hannes

It's hard to say what the problem is, the `genome.fa` is opened but no data is read in the region H1_8_48-4_1:50001-100000 while the region H1_8_48-4_1:1-50000 appears to work (no output...

Thank you for uploading the FASTA for me. I found the problem which is that my parser for the region name ("H1_8_48-4_1:1-50000") fails because it didn't correctly handle the dash...

Hello Kate, the problem is that OLD_VARIANT_ID is only stored for SVs and graphtyper consider these examples as small variants. For insertions and deletions I calculate SVLEN=length(ALT)-length(REF) and I only...

Hi sorry for the late response, I have been on a long leave. It is very possible that there are some overflows going on when working with >4GB genomes. We...

Hi. It is different failure levels, higher lever means less confident call. Basically it looks at what the other genotype models are calling and gives FT=PASS if all the models...

Hi, can you send me an example of one of the those insertions?