Questions tagged [genotyping]
Determination of the genotype (for example SNP, allele, heterozygote mutant, etc.) of a sample.
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1answer
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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....
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1answer
49 views
Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)
Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these?
For the moment I ...
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31 views
When using VCF, what is the default PL value when P(genotype) is zero
The PL field represents the normalized Phred-scaled likelihoods of the genotypes considered in the variant record for each sample. It is explained in detail (in ...
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0answers
31 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 ...
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1answer
47 views
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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0answers
147 views
What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
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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1answer
104 views
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 ...
2
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1answer
49 views
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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0answers
58 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 ...
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1answer
42 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 ...
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1answer
44 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 ...
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1answer
54 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 ...
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294 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 ...
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2answers
300 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 files ...
2
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1answer
142 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 ...
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3answers
48 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. ...
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0answers
155 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
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1answer
60 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):
...
4
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3answers
608 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
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1answer
71 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
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1answer
310 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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2answers
3k 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. ...
