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`min_kmer_covg` is almost always set to the `expected depth coverage / 10` of the first sample: https://github.com/rmcolq/pandora/blob/c16c1fac48ccdf98e0719ea003492c3fd2ec9034/src/compare_main.cpp#L41…
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Hello,
I've noticed that when I re-genotype a VCF using Sniffles2, the allele depth ended up being 0 for an insertion I'm looking at, while before re-genotyping this AD was 12, and the reads with t…
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Dear OptiType,
May I ask does Optitype support MICA, MICB typing? It work pretty well on genotyping HLA genes, but will it also work on MICA and MICB? Thanks in advance.
Yours,
Ying
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i'm getting this error while building avocado
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] avocado: A Variant Caller, Dis…
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WH version= 1.4
Hello! I have HiFi reads from PB and diploid assembly
I make two vcf files with DeepVariant (dv.vcf) and find_snv_candidates (hifi_on_primary_find_snp.vcf ). Then I genotyped b…
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## Feature request
Request comes directly from researcher on the GATK forum. Researcher requests algorithmic improvements to allow use of population priors calculated on-the-fly simultaneously with ge…
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Dear Giovanni,
Thank you for your nice software. I am using scAllele for the detection and analysis of variants using scRNA-seq. I wonder how you get the information about 0/1 or 1/1 in Figure 2E of …
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Can the proposed [/search/variantmatrix](https://app.swaggerhub.com/apis-docs/PlantBreedingAPI/BrAPI-New-Concept-Preview/0.0.0-proposal#/Genotype-Matrix-Redesign/post_search_variantmatrix) endpoint ha…
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I have WES data and single-cell data (bam files, barcodes, UMIs, etc.), but I am unable to install Singularity and can only perform matching through step-by-step execution. However, I am not familiar …
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I am using `pandora map` to align the reads against the pangenome reference and call out the variants using the `--genotype` option. I ran the pandora map command using the default (ML path-oriented (…