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:
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Nanopore Sequencing with Genotyping and AMR
I have isolates of gram positive and I am interested in Staphylococcus aureus to either do:
Amplicon sequencing using Oxford Nanopore Technology - minion (requiring primers beds and running ...
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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.
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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 ...
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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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Disabling / Removing / Excluding / Collapsing * Allele SNPs indicating an Overlapping Indel
I am trying to find a way to disable the reporting of Spanning or overlapping deletions (* allele) within the GATK trio genotyping pipeline or a way to properly deal with SNPs given the ...
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How to build hisatgenotype extra index files (.link, .locus, etc)
I'm trying to run hisatgenotype on a custom genome, originally specified in fasta format. I'm able to use hisat2-build to build ...
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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 ...
