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Dear author,
Previously, I used hapdup to get the diplod assembly based on ```Assembly.fasta```. Dose shasta new version support diploid assembly?
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Hi,
Thank you for developing this nice tool.
I have obtained hap1.fa and hap2.fa using hifiasm(HiFi +HiC reads). Next, I would like to evaluate the QV and completeness of each haplotype.
Howe…
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Hello VG Team, I am currently working with the HPRC pangenome and aiming to construct a VCF file that highlights the differences between the two haplotypes (hap1 and hap2) of the HG002 sample. Specifi…
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After #2938 goes in, we need to do something so that the user knows whether the algorithm terminated because of running out of things to do or because it ran into `max_iter`. And, give guidance in the…
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**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
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Proposal or request provided by an ICAR ADE specification user:
I am trying to determine the appropriate ICAR API schemas to use for genomic test results and disease test results.
I can see how …
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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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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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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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https://vrs.ga4gh.org/en/latest/terms_and_model.html#haplotype