4 votes
Accepted

Highly heterozygous reads mapping

I believe you may be able to map your reads, but I don't know how to do that with minimap2. I recommend running gsnap, which is more SNP tolerant and provides a number of parameters which are likely ...
3 votes

Imputing small region of the genome

I would take something like 1.5Mb either side of the SNP of interest (so a 3Mb chunk), subset that out from the target and reference panel and then perform imputation on that chunk alone. I think that ...
  • 1,290
3 votes

How to indicate the END of a haplotype block in VCF?

According to the VCF specification, haplotype blocks are defined by the "Phase Set" [PS] tag: PS : phase set. A phase set is defined as a set of phased genotypes to which this genotype belongs. ...
  • 12k
3 votes

Searching tool to calculate phase/switch error rate

Assuming your files are as you show, and the genotype field is always the 1st entry of the sample information field (the 10th), then you can just do this directly with a simple awk script: ...
  • 8,225
2 votes
Accepted

Sampling haplotypes

For simple haplotype simulation of unrelated individuals, there is Montana's venerable HapSim. The model used in that tool is simple and may be good enough for your purposes. You will need to acquire ...
  • 2,116
2 votes

Sampling haplotypes

The data in your matrix appears to be from a VCF file (For reference, see https://github.com/samtools/hts-specs/blob/master/VCFv4.3.pdf). In the VCF specification, a heterozygous genotype can be ...
  • 2,116
2 votes

How to download SNP data from specific regions, population and positions?

The HapMap website was suspended due to a security issue. Archived HapMap data is available via FTP, but it's a better idea to download up-to-date International Genome data from the IGSR website (...
  • 12k
2 votes
Accepted

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 ...
  • 1,332
2 votes
Accepted

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 ...
1 vote
Accepted

How do I infer someone's haplotype of a gene from data on several of the gene's SNPs?

It depends on the scale of the data (i.e. number of individuals, number of SNPs). Generally this can be done by matching up individual SNP genotypes to haplotype tag SNPs. The specific combination of ...
  • 12k
1 vote
Accepted

Generate an appropriate output from DNaSP6 to Arlequin program

Yes, your question makes alot of sense and its a good question because hits at the heart of differences between population genetic analysis and phylogenetic analysis. However, when you speak about ...
  • 7,980
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 ...
1 vote

How to indicate the END of a haplotype block in VCF?

Two options that immediately come to mind, depending on what you hope to accomplish down the pipeline: you might simply mark the unphased sites with a "/" instead of "|" to indicate they are not ...
  • 111
1 vote

Program to make a haplotype network for a specific gene

This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found here. The problem with manaul haplotype maps is the area of ...
  • 7,980
1 vote

How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?

I am not sure I understood all, but what you do is like doing a Markov chain but instead of saying that the previous position(s) decides the fate of the next one(s) is the block what determines which ...
  • 4,622
1 vote

How to indicate the END of a haplotype block in VCF?

There is a new idea of reporting the "phased haplotype/genotype block" with unique block ID. phaser uses "PI" (unique phase-index) and "PG" (phased-genotype). GATK is also using this idea of "...

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