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I am trying to use bcftools annotate to rename all positions in a vcf (basically, they all need to be smaller numbers to enable the vcf to be .tbi-indexed).
I have a tab-delimited file key.txt.gz f…
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Hi,
The [installation page](https://github.com/keoughkath/AlleleAnalyzer/wiki/Install-AlleleAnalyzer-and-its-requirements) suggests we need bcftools version number at least 1.5, whereas the [lates…
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Dear bcftools :
I attempted to use bcftools to generate haplotype sequences using the phased.vcf (from HiPhase), but the process was unsuccessful. Are there alternative solutions available? Below is …
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Hi! I am having a problem annotating a VCF file of structural variants. I just want to add tags to the INFO field by ID but I get this error:
```
bcftools annotate -a ${ANNOT_FILE}.gz -h ${HDR_FIL…
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Post
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Hello,
I'm getting trouble while installing MoCha with this command line.
" cd bcftools-1.20/
/bin/rm -f plugins/{{mocha,beta_binom,genome_rules}.h,{mocha,mochatools,extendFMT}.c}
wget -P plugi…
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We're working on a GPU-accelerated mpileup implementation. We have a generic algorithm working, and now we want to do actual variant calling on the results.
As an intermediate step, we would like t…
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Hi,
I am new to using bcftools +liftover, I want to liftOver from hg38 to hg19.
However, I get the error:
"Error: the reference allele GT does not match the reference NN at..."
I converted my …
ktg25 updated
1 month ago
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@sandve, I am working on reconstructing a haploid haplotype using the imputed genotypes from KAGE. Currently, I am using the following commands:
```bash
kage index -r MHC-CHM13.ref.fa -v MHC_49-M…
gsc74 updated
1 month ago
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Hi! I was trying to split multiallelic variants and keep only SNPs in my vcf file when I encountered an error message saying:
```
bcftools norm -m -any chr13.hg38.vcf.gz -Ou |bcftools view --types s…