-
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, I am trying the snakemake with your example files , but I got the Error, could you share your help? Thanks
Config file config/example_config.yaml is extended by additional config specified via …
-
I’m currently using the test VCF file you provided to create SAV files for chromosomes 18 and 20, and I encountered some issues when trying to concatenate the two SAV files.
**Attempt 1**:
I used …
-
Hi,
I am confused about `--phasing-vcf phased.vcf`, I don't know which phased.vcf should I choose.
```
severus --target-bam phased_tumor.bam --control-bam phased_normal.bam --out-dir severus_out …
-
Hello,
I am wondering how to create the input files to run this package. I have taken a look at the example data and they look a bit like STRUCTURE format (coded in 0/1/2). Is this correct? If so,…
-
In both versions 1.0.0 and 1.0.1, I have been getting VCF lines that have 19 columns rather than the expected 10 columns, as well as blank links. It appears that some lines are concatenated together…
-
Hello,
Thanks for maintaining StructuralVariantAnnotation! I'm attempting to convert VCFs to .bedpe files using the following code:
```
vcf
-
Hi，
The program only generates chunked panel data as RData files but does not proceed to the imputation step. When using a different reference panel with the same code, there are no issues; only the …
-
Hello, I have created a new account, but are not able to import. Get error
An error has occured please contact developers. :-(
Is it possible to import more vcf files at once or do I need to i…
-
Hello,
I am using popscle dsc-pileup function as a prelude for running demuxlet on cellranger output. Here is my code:
`packages/popscle/bin/popscle dsc-pileup --sam bam.bam --vcf vcf1.vcf --out h…