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Questions tagged [genotyping]

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

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2answers
88 views

Proper use of BWA MEM on multiplexed GBS sample

I have a multiplexed lane of GBS sequencing reads as a fastq file. I understand the first step is to demultiplex and trim the adapter sequences from the reads. This yields many individual fastq ...
2
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1answer
37 views

PLINK - Transposed BED file?

I'm currently working with the PLINK file system to store large amounts of genotype data. The plain format consists of three files, two files for storing phenotype and marker information as well as ...
1
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3answers
39 views

Genotyping technologies do not maintain phase?

Why exactly does genotyping not maintain phase? I guess I'm more confused on what's the difference between sequencing and genotyping, and as a result how phase is maintained in one, but not the other. ...
1
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0answers
85 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 ...
3
votes
1answer
41 views

using SNPs to identify mixed samples

Is there a way to identify mixed samples based on SNPs? Example input (table of genotypes for multiple samples): ...
3
votes
2answers
99 views

Two variants associated with same chromosomal position in genotype data for one individual

I'm trying to play around with my family's raw genetic data from Ancestry.com so that I can do some genetic analyses, and I noticed in the AncestryDNA raw data files that some regions of the genome ...
4
votes
1answer
52 views

Make ipyrad use cuda-enabled NVidia card on Ubuntu

I want to use ipyrad on a new Ubuntu machine that has an NVidia Quadro K2000 card with 384 cores. One can configure ipyrad to run on a linux cluster. Do I have any options to get ipyrad to access ...
3
votes
1answer
211 views

Techniques for analyzing and quantifying sample bleed through in genotyping with Illumina

I am looking at the presence of viral genotypes within individual samples within an assay. Often times there is a sample whose read counts are firing off the charts and this sample tends to "bleed ...
17
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2answers
1k views

Single-sample vs. joint genotyping

I am trying to understand the benefits of joint genotyping and would be grateful if someone could provide an argument (ideally mathematically) that would clearly demonstrate the benefit of joint vs. ...