Questions tagged [genotyping]

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

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Illumina Final Report seemingly giving impossible genotypes; how do I make sense of this file? [closed]

I am working with an Illumina-generated final report file from human genotyping; the MEGA chip I believe. It's in a massive .csv file I've been 'exploring' via unix commands on a compute cluster, ...
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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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What does the absence of a variant in a VCF file mean?

I have a individual.snp.vcf.gz file of an individual genome and the referencegenome.snp.vcf.gz file of the reference genome. ...
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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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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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Converting a Dante Lab VCF file

Is there an easy way to grab the rsids (hg38) of a VCF file? I know one of the tabs can contain RSIDs, but this file doesn't contain any. I have a software I created for mapping 23AndMe DTC testing to ...
Shay Maor's user avatar
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Reference for the statistical methodology used in joint genotype calling

I am searching for a good reference that explains the statistical methodology used in what is variously known as Joint Genotyping, Cohort Genotyping or Multi-sample Genotyping. One with a pseudo code ...
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Definition of genotype in demuxlet

I am reading the Online methods of the demuxlet paper. The genotype $g$ is taken from the set $\{0, 1, 2\}$, defined as "the true genotype of the sample corresponding to $c$-th droplet at $v$-th ...
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What is the best way to process yeast genomes?

I have obtained several hundred raw, unassembled yeast genomes from NCBI and I am looking for advice on how to process the genomes for downstream analysis. I have a reference genome (S288C) to use for ...
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Is there an alternative to bulked segregant analysis for insects?

This strategy seems to be most commonly used for plants. When crossing animals isn't possible, how can I do a similar study to identify a particular locus responsible for a polymorphic trait (...
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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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Why does GATK produce both 0/1 and 1/0 genotypes in the same file? Are the two not equivalent?

I have always thought that 1/0 and 0/1 in VCF genotype fields are equivalent. And yet, GATK uses both. For example, these are ...
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imputed dosage values for vcf files

I have one more question related to genotype file. I submitted the job in michigan imputation server. and my imputed dosage for chr 22 file is: 22 16050435 22:16050435:T:C T C . PASS AF=0.00098;MAF=0....
Rhea Bedi'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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Meaning of order of alleles in VCF GT field for unphased genotypes

Order of alleles in genotype field (on VCFs) can be used to infer haplotypes However, what about unphased genotypes? I have a VCF file where I only have unphased genotypes: ...
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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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genotyping or variant calling in R

Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions. I found deepSNV::bam2R which roughly does what I ...
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Excess average estimated identical-by-descent in genotype data

(Cross-post with Biostars: https://www.biostars.org/p/470788/) We have some genotype data that we are putting through quality control in PLINK 1.9. As part of this QC, we have limited the data to ...
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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 ...
Maxim Masiutin's user avatar
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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 ...
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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 ...
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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 ...
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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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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 files ...
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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 ...
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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. ...
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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 ...
Peter Pearman's user avatar
3 votes
1 answer
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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): ...
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4 votes
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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 ...
Sarah's user avatar
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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 ...
Peter Pearman's user avatar
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427 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 ...
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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. ...
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