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We aim to create the `.mu` and `.UD` resource files, which are auxiliary files for the SVDPrefix, using the CHM13 variant call format files (VCFs) available at [this link](https://s3-us-west-2.amazona…
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### Description of feature
**Description**:
I am writing to request the addition of parameters for specifying haploid contigs and regions when detecting SNPs and Indels using DeepVariant in the nf…
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All tools in 'NGS: Indel Analysis' are missing on GVL-3.05:
NGS: Indel Analysis
- Filter Indels for SAM
- Indel Analysis Table for combining indel interval data
- Indel Analysis
One tool (Indel Anal…
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Hi
I have a 38 base pair heterozygous deletion in my input VCF file which is not showing up in either the flt.xlsx or gene.mutationburden.case files once RUNNER completes so it seems to have been f…
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Hi @lrauschning,
when I run `msyd call` in `--core` mode on some potato haplotypes, I get a nice PFF file of the coresyn regions and a merged VCF for the same coresyn. The SNPs and indels which do …
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**Describe the bug**
I suspect CRISRPme is occasionally reporting off-targets generated by indels that are False-- i.e. that are not actually generated by the reported indel
As part of an analys…
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I got this error when I run the following commands;
```
singularity pull clairs.sif docker://hkubal/clairs:latest
singularity exec --bind /truba/home/erdikilic/pacbio_nd_t:/data clairs.sif /opt/b…
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My own analysis of Illumina (`SRR11140750`, bottom track) and nanopore (`SRR11140751`, top track) data from the same swab sample shows your variant analysis doesn't include indels:
![image](https:/…
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Dear Olivier,
I am wondering how well it is for Shapeit 4 to handle INDEL, CNV, STR and SV?
Thanks.
Shicheng
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Hi Giulio / All,
I tried to get +liftover going on our systems but found location of a couple of files needs to be detailed -- could anybody point to me?
They are 1kGP_high_coverage_Illumina.sit…