Brent Pedersen

See my response in #125 . If you have other questions let me know. The HTML output is supposed to help you find the male or female samples visually, the...

Hi, thanks for reporting. What tool made those annotations?

I mean what tool added `sv:intron|FMR1NB||protein_coding|+||` to your VCF?

hi @FlexLuthORF can you attach a small VCF (can be just the header and a single variant) that shows the issue?

If I run this: ``` python issue302.py 2201410002_head70.vcf.txt > o.vcf bcftools view o.vcf > /dev/null ``` I get no error. Here are the contents of issue302.py. If you can show...

This happens for you using my code above? The o.vcf is well formed with the correct headers.

Hi, the order doesn't matter. You'll have to decide post-hoc what is somatic and what is not (the genotypes won't help you there as they are for diploid samples).

Hi, can you show the actual line from the VCF? the INFO field is key=value, so you can't have the same key twice. Format fields are separated by `:` as...

That is not VCF format. It might be a text format output by annovar?

looks like this is due to numpy 2.0. We could change the type to np.uint32_t, I think. Would accept a PR