-
For discussion:
# Specification: VCF to VRS Processing Package with Cohort Allele Frequency Generation
## Overview
This package processes Variant Call Format (VCF) files to ensure compatibility…
-
View details in Rollbar: [https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5342](https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/5342)
```
UploadPipeline 7903 failed. Filenam…
-
Hi,
We have 10x data from a cell village and I am trying to identify donors in the village using donor assignment. I have the 10x bam file, barcodes.tsv, gtf and vcf files.
Step 1: I ran Drop-seq…
-
When converting the VCF spruce data to Zarr I noticed that even the longer chromosomes (>1.2Gbp) are encoded as 32-bit integers. In the text I wrote that the maximum value of VCF POS is ~537Mbp (God k…
-
Hi,
When I run pyRona using my data, I always get some errors, do you have any suggestions to solved this problem ?
command line I use: "pyRona lfmm -pc 4bio_current_env_pop.txt -fc 4bio_access_cm…
-
Hi! I have been trying to convert my genind file to hierfstat so I can calculate some population statistics but I keep on getting an error when I run my code. Here's the error:
```
Error in (funct…
-
## Describe the issue
I'm annotating a vcf coming from Manta. In the output, some of the variants are not annotated and I don't know why. In my vcf, all the variants have all fields information (incl…
-
**1. What were you trying to do?**
```
vg giraffe --output-format gam --gbz-name $vg.gbz --minimiser-name $autoindex.min --dist-name $autoindex.dist -f $R1 -f $R2 -t $threads $reference.fa $vcf.gz…
-
In our initial use case, we have the comfort of a deterministic mapping between chromosomes and actual VCF files, i.e. `chr4` always exists only on a specific file named in a GREGoR data table.
I'm…
-
Hi,
I am currently benchmarking tools that balance "compression and accessibility" for genotype data and encountered an issue when using XSI with large datasets. I hope you can assist me in resolvi…