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Testing has shown that some samples are not assigned any genotype based on the kmer scheme file but are correctly typed using the SNP scheme. This is likely the result of a missing partial assignment …
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Hi,
I have suggestions for "OBI:0000435" - "genotyping assay" term and some of the terms under it.
"Genotyping assay" has synonyms that include snp, which is limiting and confusing, so I'd remo…
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Hi,
I wonder how the genotypes of the parents are corrected using the progeny allele counts. I guess with "correct_variant_types()", in offspringscoring.py? What I find strange is that on my VCFs s…
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Suggested by Peter Du, who observed that HaplotypeCaller finds ~3400 snps (~7700 snps + indels) in a mouse exome, vs. ~2000 hets found by CollectAllelicCounts + naive genotyping. See related issues #…
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Hello, I need some technical assistance. I have a genotyping results for a number of SNPs (rs.....) and associated allele 1 and allelle 2 base calls for NA12878 and NA12877. I'm trying to find where…
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It would be nice to add a vignette that goes from reading in data from a VCF file to genotyping and filtering SNPs.
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Hi, thanks for developing this tool for genotyping. I performed SNP calling with cellsnp-lite, with either (7.4M SNPs with minor allele frequency (MAF) > 0.05) or (36.6M SNPs with minor allele frequen…
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Hello,
Thank you for creating this useful package (and also the genotyping package, cellsnp-lite) that has been critical to my work in bone marrow transplant research.
I have ran the vireo packa…
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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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We are trying to use genotyping arrays (Axiom) to get VCFs for demuxlet.
Are there any recommended steps / tutorials for SNP cleaning and filtering to optimise the demuxlet yield?
We are curren…