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Dear Kieran,
Thank you for this wonderful tool!
I have been using Pixy with standard, well-annotated VCFs, and everything goes correctly. Nevertheless, when I process my VCFs with PLINK, the Pixy …
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
Yes
**Describe the issue:**
**Setup**
- Operating system: Ubuntu 20.04.6 LTS
- DeepVariant ver…
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When trying to run HapNe-IBD as recommended by guidelines on a standard set of human WGS (n=25), using the provided code in a file called split_vcf_chr_arm.py:
`split_vcf(vcf_file='./vcf_phased', sav…
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when following the tutorial at the step ds.ingest_samples(sample_uris = batch1_uris) I get the error:
RuntimeError: TileDB-VCF exception: Cannot open VCF file; failed to load BCF index.
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Hi,
I am running `cactus-graphmap-join` with `--vcfwave` and found an empty output VCF for one chromosome in the working directory. It is due to the input VCF is truncated. However, `vcf-bubwave` c…
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Some errors:
```
tests/test_vcf_examples.py:846:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _…
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Dear all,
So I've tried using LDBlockShow on a QTL dataset to visualize the linkage blocks between biallelic SNPs.
I tested to observe the blocks before and after pruning to understand how the pru…
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bcftools norm -m- -o Mutect2_split.vcf -O z
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### Operating System
Other Linux (please specify below)
### Other Linux
Red Hat Enterprise Linux 9.4
### Workflow Version
2.2.3
### Workflow Execution
Command line (Local)
### Other workflow e…
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Hi,
I am using evaluate_SV_overlap_calls.pl to evaluate Delly and Lumpy SV calls against Sim-A reference sets, and I use the following command:
perl EvalSVcallers-master/scripts/evaluate_SV_over…