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10 votes
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Single-sample vs. joint genotyping

Say you are sequencing to 2X coverage. Suppose at a site, sample S has one reference base and one alternate base. It is hard to tell if this is a sequencing error or a heterozygote. Now suppose you ...
user172818's user avatar
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3 votes
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What does the absence of a variant in a VCF file mean?

The absence of a variant means the variant was not found. However, that does not mean you can assume the position in the sequenced individual was homozygous for what is in the reference. Perhaps the ...
terdon's user avatar
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3 votes
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Meaning of order of alleles in VCF GT field for unphased genotypes

In the case of unphased VCF 0/1 and 1/0 are exactly equivalent and the order has no meaning. Throughout the VCF specification, ...
JRodrigoF's user avatar
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2 votes
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Two variants associated with same chromosomal position in genotype data for one individual

First of all, take these data with a very large pinch of salt. This sort of targeted analysis is not designed to produce high quality genetic data but, to give an idea of a sample's ancestry. Given a ...
terdon's user avatar
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2 votes

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

It's pretty common for SNPs and indels that map to the same position in the genome to be assigned different rsIDs, particularly when the indel spans multiple base pairs in the reference. You can get ...
heathobrien's user avatar
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2 votes

Make ipyrad use cuda-enabled NVidia card on Ubuntu

You would have to get CUDA Python set up on your system and likely modify ipyrad to actually use it (for example, by incorporating numba). So while this is possible, it will require significant effort ...
Devon Ryan's user avatar
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2 votes
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Genotyping technologies do not maintain phase?

Phasing means that you are able to distinguish the both copies of your target sequence. (Usually you have one from your mother and one from your father). If you can do this, depends mainly on the ...
finswimmer's user avatar
  • 1,342
2 votes

using SNPs to identify mixed samples

Yes. The general term for identifying subsets from a mixed group is deconvolution. This is easier to do when there is haplotype-level information available (e.g. sequenced reads that span multiple ...
gringer's user avatar
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2 votes

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

You need to understand a few key points for your example given: (a) Ancestry (and 23andMe) will use the letters I and D to indicate it is an InDel/DELINS. You have to read the rsID definition to ...
SurplusGadgets's user avatar
2 votes
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PLINK - Transposed BED file?

Yes, this exists, and can be efficiently generated by plink 2.0's --export ind-major-bed command. (The third byte is 0 instead of 1, and the specification is ...
Christopher Chang's user avatar
2 votes
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What is the best way to process yeast genomes?

What is your data type? Many assemblers can resolve heterozygosity. PacBio HiFi reads can be used with hifiasm to resolve both haplotypes rather trivially. This is the best case scenario and older ...
Maximilian Press's user avatar
2 votes
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Is there an alternative to bulked segregant analysis for insects?

I'll have a go at answering this. I don't understand beetles within Insecta: I am well aware they very distinct, obviously in phenotype and ecology, but also genetically. I think they have unique ...
M__'s user avatar
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2 votes

Why does GATK produce both 0/1 and 1/0 genotypes in the same file? Are the two not equivalent?

Convention The convention is it should be in ascending ordering, i.e. 0/1. The question is, why the convention broken? Phasing I think, at a guess, the answer is it depends what reference genome you ...
M__'s user avatar
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2 votes

Reference for the statistical methodology used in joint genotype calling

Here is a recent example of the derivation of the genotype model from Octopus genotype calling paper: All samples have known ploidy and copy number, so the likelihood function of reads $R$ given ...
user438383's user avatar
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2 votes

Reference for the statistical methodology used in joint genotype calling

To the best of my knowledge, the first joint calling model was published by Le & Durbin (2011) and refined in Li (2012). They come with detailed derivation. Both samtools and older GATK are using ...
user172818's user avatar
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1 vote
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Converting a Dante Lab VCF file

If your file doesn't contain the rsIDs, you can use a tool like Ensembl's VEP to annotate the file and get rsIDs as well. Of course, not all variants have an rsID so don't expect to find one for ...
terdon's user avatar
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1 vote
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Definition of genotype in demuxlet

The genotypes $\{0,1,2\}$ are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from supplementary resources). This is also mapped to the number of alterations (e.g., 0 -> 0 ...
gc5's user avatar
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1 vote
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imputed dosage values for vcf files

When i was still working in the field of genotype imputation, a dosage was the expectation (average) of the (posterior) genotype probabilities, coded as GP in the OP's VCF. I once contributed code to ...
winni2k's user avatar
  • 2,286
1 vote

genotyping or variant calling in R

Samtools/bcftools/tabix is available in R via Rsamtools. SEQprocess also provides wrappers for different tools such as GATK and bowtie. More utility packages are noted here.
Maximilian Press's user avatar
1 vote
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Excess average estimated identical-by-descent in genotype data

A clear negative association within an inbreeding coefficient suggests convergent evolution driven by shared selective pressure. There is an outside chance of purifying selection, or else balancing ...
M__'s user avatar
  • 12.6k
1 vote

Database of RNA-Seq and SNP genotyping data

Human RNA-seq data, like genetic data is very sensitive data as it can be used to identify people (and their relatives), so people will likely not distribute it without entering a formal agreement ...
citronrose's user avatar
1 vote

Phasing partially phased genomic data

Answer from @user438383, converted from comment: I would recommend checking out shapeit4 as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for ...
1 vote
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Can someone recommend software for reference-based genotype-estimation?

In case anyone was interested, a new piece of software for rapidly imputing and phasing low coverage sequence data from genotype likelihoods has just been released. It is called GLIMSPE and is exactly ...
user438383's user avatar
  • 1,689
1 vote

Proper use of BWA MEM on multiplexed GBS sample

The first thing to do is to group the FastQ files together following this post. Once you have your reads grouped, you could trim your files before mapping. Then you could perform your BWA alignment. ...
user324810's user avatar
  • 1,125
1 vote

Genotyping technologies do not maintain phase?

Many (small) variant calling algorithms use pileups to genotype variants position-by-position. This approach alone is insufficient to phase adjacent variants. However, if the variants of interest are ...
Daniel Standage's user avatar
1 vote

Single-sample vs. joint genotyping

The benefit to additional samples is seen in your point 1. The likelihood of making a variant call is a function of (1) the depth of coverage supporting a given variant (ignoring mapping/base quality ...
Devon Ryan's user avatar
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1 vote

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

For different variation type at the same location, each variation type is being assigned its own rsID by the dbSNP maintainers. In your example, one chromosome in the pair has a single-nucleotide ...
Maxim Masiutin's user avatar
1 vote
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Techniques for analyzing and quantifying sample bleed through in genotyping with Illumina

Are you using dual-index barcodes with different barcodes at each end? There is a known phenomena of "index switching" that occurs in Illumina reads. One way to control for this is to add in ...
gringer's user avatar
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