Hannes Pétur Eggertsson

Hey, you would need select the ~17k SNP a bit differently such that you have more SNPs in close proximity (less than the insert size) to each other because read_haps...

Yes of course. Enjoy your holidays.

Hey Lasse, Thank you for looking into this. But I did not see any contigs in the Manta VCF which are not part of the reference I am using. Here...

Things seem to be working alright by skipping the decoy sequences in Manta.

I support the idea of wrapping libStatGen in a namespace. It fixes conflicts and makes your code clearer to read, especially if you are using many different libraries. However, in...

Not always, there are some differences. The API is quite different, and in my opinion much clearer in libStatGen. But it is also missing some functionality, for example I don't...

> > Can you describe the MD field? > > It's a single integer field described as "Read depths of multiple alleles." Maybe @hannespetur can shed some more light? Yes...

Using `--sparse-fields GT,MD --pbwt-fields AD,DP,GQ,PL` over default options is improving the compression ratios quite a bit. In most of the benchmarks, running savvy master build not using the --pbwt-fields option...

> I have a 200k data set that I can use to try to reproduce. Are your smaller datasets merely sample subsets of the 200k dataset? If so, are monomorphic...

The `-10` option helped a lot. It improved the 200k compression ratio by a factor of 2.1x vs no `-10` option. `-6` and increasing the block size did almost nothing...