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Can reject in vcf_clean_and_filter
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I have a vcf.gz(single cells snp information) and a donor snp.vcg.gz.I want to use viero mode2,Here is my command:
vireo -c $cell_sampe.vcf.gz -d $donor.sorted.vcf.gz" -o ./ -N 4 --randSeed 2 --g…
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Is there a way to make the data files uncompressed?
### Examples
```shell
# Current
•/vep -i variants.txt -o variants_output.txt --gff 'data-gff.gz' --fasta 'genome.fa.gz'
# Requested
•/vep -i…
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We've had MANIFEST files nearly since the inception of the Data Store (actually, the content was originally included in the README file in each collection, but we decided early-on to move the per-file…
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Hi,
I'd like to view VCFs from the 1000 Genomes Project in IGV (version 2.17.4 with Java included) but a couple of them won't load, with an error message:
"Error loading [URL]: Unable to parse h…
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As predicted @tomwhite we've hit https://github.com/sgkit-dev/vcf-zarr-spec/issues/11 pretty quickly when adding tests on real VCF files. I added a quick cludge to workaround the first case I hit, but…
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@jodyphelan we have some indications that 1S6110 insertions may be involved in BDQ resistance
We have some ideas on how to solve this but we have some questions in terms of constructing a vcf tha…
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See the description of the `PSL` field https://samtools.github.io/hts-specs/VCFv4.4.pdf#subsubsection.1.6.2. This isn't defined explicitly as raised in https://github.com/samtools/hts-specs/issues/705…
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Hello. I encountered a very basic problem but I do not know how to fix it. I would appreciate it if you could help me. Thanks in advance. In my hapmap files, which converted from vcf, there are 2 nuc…
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Hello, I am trying to use seqVCF2GDS to change vcf to GDS files, and am getting the following error:
Error in seqVCF2GDS(vcf.fn, "chr1.gds", storage.option = "LZMA_RA", parallel = FALSE) :
std::ba…