Questions tagged [genotyping]

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

Filter by
Sorted by
Tagged with
1
vote
1answer
33 views

Database of RNA-Seq and SNP genotyping data

I need to obtain publicly available RNA-seq + SNP genotyping data for a cohort - ideally one where the RNA-seq data has been sequenced from brain tissue. I have found CMC and GTEx to be sufficient ...
0
votes
0answers
25 views

Phasing partially phased genomic data

I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since ...
2
votes
1answer
41 views

Can someone recommend software for reference-based genotype-estimation?

Problem: I have low-coverage sequencing data from humans in vcf format. For each sample, I have PL scores / preliminary genotype calls from the software ATLAS (it's a bit like GATK for those who don't ...
1
vote
0answers
49 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 ...
0
votes
2answers
157 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
votes
1answer
57 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
vote
3answers
41 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
vote
0answers
114 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
47 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
214 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
56 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
234 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 ...
19
votes
2answers
2k 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. ...