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Original request:
Adding BCF support in Notes is a feature most users will expect and it would also be useful for Swiss Property model quality checking ([user requirements](https://docs.google.com/do…
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I have been playing around with pyVCF and found I was able to read in bcf files by adding the following lines to the reader object:
```
if fsock:
self._reader = fsock
if filename …
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Hi! I'm trying to obtain a bcf using this command:
```
$pth_angsd/angsd \
-GL 2 \
-out $pth_o/$o_name \
-rf $bedfile \
-nThreads $threads \
-snp_pval 1e-6 \
-doPost 1 \…
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Hi, after I run `GLIMPSE2_phase` to impute chunks then use `GLIMPSE2_ligate` to stick them together. Unfortunately, I run into a bug:
![image](https://github.com/odelaneau/GLIMPSE/assets/141545014/79…
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Hi,
The final vcf is giving me these errors when I look at it with bcftools:
[W::bcf_hrec_check] Invalid tag name: "'SampleID'"
[W::bcf_hrec_check] Invalid tag name: "Compound_htz(sample)"
[W::b…
gevro updated
4 months ago
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Could you clarify what data is contained in `spl.tsv`? Are they the name of column in bcf/vcf? Tumor-ID, Control-ID?
And can you upload the `svs.bed`?
Thanks,
Coax
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Section 6.3.1 of the VCF 4.3 specification document has the BCF variant record fields in the wrong order. After rlen, the correct ordering of the next three fields is qual, n_allele_info, n_fmt_sampl…
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**Describe the bug**
Formatting of context description doesn't have bullet points
**To Reproduce**
Module 3 of the flight plan, the block at 10 minutes and also in BOR 2 unpacking
**Expected …
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There is a lot of shared code between bcf v2 and v3 and we should move it to some common place so it will be possible to maintain it in a more sane way, now every change should be implemented twice re…