Jared Simpson
Jared Simpson
Hi, Sorry but it hasn't. I'm travelling again now so it will take a little more time. Jared
Commit 5a4939d will emit `.` for the genotype when TotalReads is 0
The `--genotype` argument appears to be handled properly: ``` variants: option '--genotype' requires an argument ```
I'd like to add full support for read groups in the future but I can't do it right now. I'm going to leave the genotype column as "sample" for now.
Thanks for the note, yes the script should now look for `num_motifs_in_group`. We'll update the tutorial script. In the meantime, you can make the change in your version. Jared
can you send me the VCF record for the `-s 0.8` file, when the SNP was called?
Sorry I have not had time to work on this issue (or SNP calling in general). > On May 21, 2019, at 5:49 AM, herrroaa wrote: > > @jts any...
Hi! 1. I have a merge-branch ready but haven't had time to fully test it. I'll try to get to it this week since it is reading week so I...
Hi @marcotoffoli, Sorry for the slow response. The genotypes are set based on the likelihoods that nanopolish's HMM calculates, rather than `SupportFraction`. This can lead to (hopefully rare) cases where...
Hi @Blosberg, For simplicity of our code we convert all Us to Ts when loading the input fastq. Now that you point this out, I realize how this can be...