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We noticed the presence of such line in *.vcf result file:
`chr1 13116 . T G 15.23 PASS P GT:GQ:DP:AD:AF:PL 1/1:15:27:18,9:0.3333:22,27,0`
With AD of 18,9 shouldn't the GT be heterozygous (0/1) a…
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Hi,
I am trying to run DeepVariant 1.2.0 on a few human samples PacBio HiFi data (about 30x coverage per sample). I first ran my samples through the [PEPPER-Margin pipeline r0.4](https://github.com…
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incorporate / test octopus variant caller:
https://www-nature-com.insis.bib.cnrs.fr/articles/s41587-021-00861-3
https://github.com/luntergroup/octopus
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incorporate / test HELLO variant caller:
https://github.com/anands-repo/hello
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04311-4
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Spreekt u Engels? Hope you're well friend!
I'm trying to use slivar for DeepTrio calls. They are called individually as GVCFs. I then merged them using `bcftools merge -0` and ran slivar using the …
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Hi,
I have a clean install of bcbio and everything went fine with installation and no errors. While I tried to run sample it gave the following errors
```
[ec2-user@isamples]$ /newvolume/bcbio/…
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Hi everybody,
I've been trying to calculate Fst between two populations, but I got stuck at the first step: obtaining the saf files.
I start with a vcf file (coming from GATK and a subsequent fi…
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Hello,
I want to suggest here to left-aligne indel in the DeepVariant output VCF / gVCF to avoid the issue described below.
I'm running DeepVariant v1.1.0 on a set of samples sequenced with Illu…
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**Describe the issue:**
I follow the quick start guidelines, and meet this error.
**Setup**
- Operating system: MacBook Air (M1, 2020)
- DeepVariant version: 19.03.14
- Installation metho…