-
Hi!
My python version is:3.9.12 and the version of whatshap is 1.6.
I install the tool via conda
I use the following command
`whatshap polyphase unadjusted.vcf 0.bam.sorted.bam --ploidy 3 --ref…
-
We need to confirm the final contents of the string to digest. Right now, I think we had settled on these elements:
## contents
- name (*e.g.* `chr1`)
- length
- topology
- sequence digest (re…
-
**1. What were you trying to do?**
I am trying to create an index for a gfa generated with PGGB.
**2. What did you want to happen?**
With the majority of the chromosomes I'm working with the …
-
Hi `smoothxg` team,
I am trying to use `smoothxg` to smooth a huge graph (~131 Gbytes in `.gfa`) from seven haplotypes of different species of the same genera. Although they are just a few individu…
-
Hello, does `bcftools csq` support multi nucleotide variants?
This MNV `1-201363379-CC-AA` produces the CSQ below when run in local mode
```
missense|TNNT2|ENST00000660295|protein_coding|-|162EE>…
-
### What happened?
Follow up on #13445 - I almost succeed to install hail on AWS but still have some environment issue:
* I am trying to install Hail v0.2.124
* on AWS EMR v6.9.1 (latest version …
-
Dear vg staff,
After constructing the genome graph, I'm going to use short-reads sequencing data align to the genome graph using **Giraffe**. My short-reads data are likely produced by **BGI** plat…
-
Hi there,
I generated a graph for five human individuals with the following command:
```
pggb -i /g100_scratch/userexternal/mungaro0/pangenomes/pangenome_ref_guided_pggb-v4.fa.gz -o /g100_scratch…
-
following a user inquiry about data that used to be available from Noble, I ran the dataset from
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1718-7
(SRA study accession SRP055…
-
Hi,
My labmate and I have been using your `whatshap compare` tool for evaluation of phasing, using the GIAB HG002 VCF as a reference, and it has been very convenient. However, we would like to be a…