-
https://github.com/NBISweden/GenErode/blob/main/workflow/rules/9_merge_vcfs.smk#L266C23-L266C42
This command does not remove sites that are coded as heterozygous sites but are fixed derived sites (…
verku updated
4 weeks ago
-
Investigate whether VCF files downloaded from the GDC portal work with the [vcf track type](https://jbrowse.org/docs/variants.html).
Note: VCF tracks require the VCF file to be gzipped and an index…
-
Hi,
I am struggling with filtering large number of false positive variants from output of Vardict-Java, and find this very good tool may be helpful for me. Now, I am using the docker image cpwarde…
-
[Lingchenjin@mu01 Example2]$ ../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS gwas.pvalue -OutPng -SeleVar 2
#Detected VCF File is phased f…
-
If vcf looked for a $VCF_FILE envar, then the source-file/folder could be omitted.
./vcf.sh jane ~/contacts/*.vcf
becomes (after putting it in the $PATH)
vcf jane
Other *.vcf files/folders cou…
-
### Describe the bug
Export of a contact converts spaces in its prefix into `\,`, causing 3rd-party clients to render what should be spaces as ",".
### Steps to reproduce
1. Create a contact …
-
Thank you for creating this pipeline. I've installed all the necessary components and I'm currently attempting a test run to demultiplex a single pool of 10X multiome data, which includes four multipl…
m571c updated
3 months ago
-
The below files only contain chr22 or chrY and the compression is messed up. nref=0 in the index. We should catch the error and handle rather than opening app.
http://vcf.iobio.io/?vcf=https://s3.ama…
-
Hello
I tried using your program, but i keep getting the error
Traceback (most recent call last):
File "/home/pato/miniconda3/envs/vcf_anno/bin/vcf-annotator", line 393, in
annotator.ann…
-
Hi!
I am trying to ingest samples, but run into the following problem:
```
_40b48cf415984c70a4ab49e225d7c8ef_21 samples = SAMPLE
[2024-02-13 09:59:31.061] [tiledb-vcf] [...] [debug] Finalizing la…