Questions tagged [genotyping]

Determination of the genotype (for example SNP, allele, heterozygote mutant, etc.) of a sample.

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What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?

This question was also asked on Biostars Consider this minimal VCF file which contains a multi-allelic call made by a somatic variant caller on a human tumor sample: ...
terdon's user avatar
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Does pooled sample genotyping microarray analysis exist?

I want to genotype samples in small batches with a common microarray (e.g., the GSA). However, the cost is very high for small batches. With a higher sample throughput/volume, per sample cost becomes ...
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RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. ...
Tom's user avatar
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Genotype quality in VCF for haploid calls

I cannot find in the VCF specs what is the default value of Genotype Quality GQ for haploid calls. In such case, is the default the missing value ...
gc5's user avatar
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Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes

I have a tab-separated file (the columns are rsID CHROM POS GENOTYPE) generated by Diganomics with Illumina GSAMD (v2.2) from male DNA, and there are a few hundred loci within X or Y chromosome that ...
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Running IBD using PLINK --parallel (v2)

I have merged two huge .gen files with roughly 500k samples in total - around 3 TB. I wish to run an IBD (identity by descent) check to identify if there are ...
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GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
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Convert genotyping results to vcf or other plink formats

I used a Genotyping software called T1K to generate KIR genotyping, the output file contains genes and alleles for each sample, how can i convert the results to a vcf file or other formats which can ...
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Combine gvcf for whole population or for different phenotypic groups?

I created 400 or so gvcf files (g.vcf.gz) using the gatk HaplotypeCaller. These files show populations for three distinct traits (HR, MR, HS). Now, I want to use gatk GenomicDBImport to combine gvcfs ...
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