Questions tagged [genotyping]
Determination of the genotype (for example SNP, allele, heterozygote mutant, etc.) of a sample.
9
questions with no upvoted or accepted answers
2
votes
0
answers
538
views
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:
...
- 9,662
1
vote
0
answers
41
views
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 ...
- 513
1
vote
0
answers
37
views
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.
...
- 11
1
vote
0
answers
100
views
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 ...
- 1,783
1
vote
0
answers
93
views
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 ...
- 151
1
vote
0
answers
607
views
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 ...
- 836
1
vote
0
answers
207
views
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 ...
- 183
0
votes
0
answers
59
views
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 ...
0
votes
0
answers
76
views
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 ...
- 51