-
For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.
-
### Description
As documented in #93, vcztools view is not running as fast as bcftools view on real genome data. I reproduce the performance data below.
This issue tracks understanding the perfo…
-
View details in Rollbar: [https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326](https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5326)
```
Traceback (most recent call last):
…
-
Hi @kcleal,
I'm seeing some weird behavior from Dysgu around read counting and was curious if you could help. I'll preface this by saying the sequencing data I'm working with is not WGS/WES but i…
-
## Bug Report
### Affected tool(s) or class(es)
GenotypeGVCFs with `-all-sites`
### Affected version(s)
- 4.2 through 4.6
### Description
We tried to run GenotypeGVCFs from GATK 4.5 with …
-
Hi,
I noticed you currently use version 4.3 of the VCF specification for tandem repeats. However, version 4.3 does not provide guidelines on handling tandem repeats, whereas version 4.4 does. Do y…
-
Hi Simon, I'm curious about your thoughts regarding how filtering a VCF file for LD and phasing might influence the results of ABBA-BABA tests. I have played around with different filtering parameters…
-
### Verify
Can you see anything in the logs?
Make sure your issue is not already in the [htsjdk issue tracker](https://github.com/samtools/htsjdk/issues?q=)
### Subject of the issue
In htsjdk 2.1.0…
-
add class function called `def sort` so `vardict filter_single` and `vardict case_control` return vcfs sorted on chromosome and position. Sort should be called for the command [here](https://github.c…
-
I followed the [tutorial](https://odelaneau.github.io/GLIMPSE/docs/tutorials/getting_started/) and all works! except building on linux :( and few minor updates on bash scripts.
I used GLIMSPE2 from …