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 ...
- 316
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 ...
- 1,679
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. ...
- 13.8k
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:
...
- 9,662
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 ...
- 2,236
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 ...
- 2,236
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 (...
- 13.8k
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 ...
- 1,342
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 ...
- 3,804
1
vote
Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?
HaploSep uses allele frequency data - I presume you have genotype data.
In that case, I would suggest looking at either Beagle5.2, shapeit4 and Eagle2. I believe they more or less give the same ...
- 1,679
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 ...
- 13.8k
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 ...
M__♦
- 11.9k
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 ...
- 5,060
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 ...
M__♦
- 11.9k
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 ...
- 4,693
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 "...
- 200
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