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5 votes
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Does phasing improve imputation quality?

Yes. Phasing data leads to a better imputation accuracy. More specifically: Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and ...
JRodrigoF's user avatar
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4 votes
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Using Beagle 4.1 for phasing and IBD - chromosomes

OK, I ended up contacting one of the authors of the program, who kindly answered to my question: Either approach should work, [i.e. running the analysis by chromosome vs joining the data together] ...
Max_IT's user avatar
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3 votes
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Tutorials on phasing and imputing low-coverage sequencing data

This is all relevant for data 0.5x-1x coverage. Assuming you have genotype likelihoods data, if you want to phase low-coverage data, the most suitable options are GLIMPSE, Beagle4 and QUILT. Of the ...
user438383'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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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: ...
terdon'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
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2 votes

Q: What analyses can I perform with a completely phased genome assembly?

Some population genetic inference methods require the data to be phased because they look for long stretches of matching alleles between individuals, rather than just matching genotypes. Here, '...
user438383's user avatar
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2 votes
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Are the GIAB reference genomes (HG00N) fully phased?

As the two alleles in a genotype are separated by / but not |, the main v4.2.1 VCF is not phased. The README says the phased ...
user172818's user avatar
  • 6,545
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
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Interpreting imputation result from GLIMPSE

It seems that you didn't use the following flag: ...
user438383's user avatar
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1 vote

How do I install shapeit4 on Ubuntu/Mint?

Manually editing makefiles is just... ugh. Save yourself the effort and use conda: conda create -n shapeit conda install -c bioconda shapeit4 -n shapeit
user438383's user avatar
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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 ...
user438383's user avatar
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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

Read-informed statistical phasing

shapeit4 is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads ...
user438383's user avatar
  • 1,689
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

Using Beagle 4.1 for phasing and IBD - chromosomes

I would also add that splitting your data into chromosomes allows you to run each chromosome in parallel (presuming you have some kind of server you can send each run to), vastly reducing the amount ...
user438383's user avatar
  • 1,689

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