Jonathon LeFaive

Haider, I don't see the attachment.

Thanks I just pushed a fix for this to statgen/savvy. Please run the following and then give it another try: ``` cget remove statgen/savvy --yes cget install statgen/savvy@9ba1ab13e8afdbd09d4ae63bdf9fd0ac63229f99 cd build...

Since your container is always building with the latest from savvy, you could just rebuild the container image without modifying the definition file.  - JLOn Feb 24, 2023, at 15:40,...

The license is a little hidden: https://github.com/statgen/bamUtil/blob/master/copyrights/COPYING

HDS is the sum of posterior probabilities (see equation 4 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5157836/) for templates with alternate alleles for that variant. This paper is for Minimac3. While Minimac4 has minor differences,...

@steffenom, thanks for reporting this. The earlier conversation was regarding v4.0.x. You are using v4.1.x, and this feature was missing from the new version. I just pushed a fix to...

For the IDs with CHR:POS, are these variants that exist only in the target file (not in reference)? If using --all-typed-sites, IDs for such variants are carried over from the...

I see. FYI, you can generate an msav directly from a VCF, BCF, or SAV file with `minimac4 --compress-reference input.vcf.gz -o compressed_output.msav`. This still needs to be documented in the...

There may be a small difference with smaller reference panels (tens of thousands of samples). By default, `minimac3 --processReference` does parameter estimation and saves those parameters in the m3vcf. This...

> Error: Cannot write empty block > Error: serializing final block failed @buegelbeatz , this should be fixed with https://github.com/statgen/Minimac4/commit/6f9f1404e1875f9e7773af493872c4d94efc105f