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When I try to process the resulting VCF file with bcftools, (for instance a simple `bcftools view`) I get this kind of errors:
, and each XY individual wou…
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Hi. @kaichop
I want to update the clinvar to version 20241111. I've run the code below by following the documentation:
```
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20241111.…
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For discussion:
# Specification: VCF to VRS Processing Package with Cohort Allele Frequency Generation
## Overview
This package processes Variant Call Format (VCF) files to ensure compatibility…
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Hi,
I've been using PopLDdecay to analyze LD decay across multiple populations (7), but I'm noticing a wavy pattern in the decay curve that seems unusual. I would like to achieve a smoother LD deca…
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### Description
I aligned all my genomes using an older version of Anchorwave (before 1.2.3), so now when I call `phg create-maf-vcf` I have to use `--legacy-maf-file`. I noticed the output has chang…
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### Description of the bug
After I got snp vcf files from strelka, freebayes, mpileup, and haplotypecaller, I tried to annotate them by snpeff and vep. Finally, the vcf file from haplotypecaller was…
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-b, --bed BED file with repeat coordinates
-o, --out Output tsv path
--trid TRID of a specific repeat to analyze, should be in the BED file
-@ …
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Hi - When I try to index multiple VCF files data/*.gz, it only takes the first VCF file for indexing and not all in the directory. Can it only take one input VCF file at a time?