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@ntm
Nicolas,
Thanks for your patient reply!
I fixed the dbNSFP and Transcript problem with your help. Really exciting!
However, when I run the secondary.pl, the final result of four file folders …
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Hi,
I've been working on using the snpArcher pipeline for some variant calling and have run into an issue that I'm not really sure how to address. Most of the pipeline finished running but there see…
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After three hours of running the test pipeline, output hangs at
````
[fa/fd89fd] process > preproc:prep_ref:wget [ 0%] 0 of 1
[- ] process > preproc:prep_ref:mmi -
[05…
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I am trying to use deepvariant to call variants using a TPU Node v3-8, but I am running into a persistent issue.
Here is the command I am using:
```bash
docker run \
-v `pwd`:`pwd` -w `pwd` …
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Hi bcftools developer,
I am trying to change the genotype and therewith (in my case) the ploidy based on the VAF of a call. The command I am using is the following
```bash
bcftools +setGT in.bc…
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freebayes v1.3.4 bailed on me writing this to stderr:
Hit end of chr, but still attempted to call location !!!
Breaking
This seems like an internal problem, maybe a bug? It
happened when I a…
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.3/docs/FAQ.md**: Yes
**Describe the issue:**
(A clear and concise description of what the issue is.)
Running singularity …
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Hi. I am now using my own data. But I have a problem in step 1. It seems that the program cannot finish this step to generate the _parsed.vcf.gz files for the parents.
I also tried using gvcf files,…
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There appears to be a loss of lines of data when -g 10 is used to group blocks together.
* When -g 10 is not used, the issue is resolved with bcftools 1.11 because the missing data is included in the…
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I think the workflow referenced in the example [was deleted](https://github.com/gatk-workflows/gatk4-germline-snps-indels/commit/c8d0d63baa878ea4991e3108dd04e2c3bdbae6d2). Tried using and the script …
kinow updated
2 years ago