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Hello dear developers,
I have run PECAT on a diploid plant genome (heterozygosity=3.3) and obtained a primary (4.7Gb) and alternate (2.6Gb) set and haplotype1 (4.7Gb) and haplotype2 (2.8Gb). Do yo…
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Post-Shapeit4 vcfdist metrics looked good despite remaining issues with overlapping alleles, suggesting that perhaps vcfdist may not be sensitive to this (or at least not when running in its default m…
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Hi, I mmeet an error like below, I have no idea why this happens, I asked ChatGPT and it told me that in this position, it contains both haploid and diploid genotypes, But I checked the target.vcf fil…
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When I use --ehh to calculate the EHH curves for the ancestral and derived haplotypes, I think the result is wrong.
e.g. for chrxxx:G:A, In my vcf, allele count for A (derived) is 15 and for G (ances…
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We commonly would like to be able to investigate which haplotypes carry which mutations, particularly non-synonymous SNPs and CNVs. This is usually in the context of investigating a locus under recent…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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Hello,
I encountered into some problems while using this tool from Docker to call SV from assembly-hap and I tried many times and still couldn't make it. If you can give me some suggestions, I'd appr…
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https://vrs.ga4gh.org/en/latest/terms_and_model.html#haplotype
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Hi, i'm testing GAUDI running it to more than two ancestry. To check this before using real data, I changed the msp files from the toy data manually, changing some numbers 0 and 1 to 2 or 3. I am not …
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Hello, I ran "selscan --xpehh --vcf vcf1_Chr1.gz --vcf-ref vcf2_Chr2.gz --pmap --out outfile", but no files were generated.
The result of the operation is:
selscan v1.3.0
Opening vcf1_Chr1.gz...
L…