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Questions tagged [phasing]

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-2 votes
0 answers
29 views

pharmacogenomics diplotype calling for CYP2D6 gene from a WES sample

I am currently working on pharmacogenomics diplotype calling for CYP2D6 gene from a WES sample (HG02373) from 1000 genomes, using Aldy4 v4.5, python v 3.11, OS used here in ubuntu linux v22.04, using ...
0 votes
1 answer
52 views

Does phasing improve imputation quality?

If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
1 vote
1 answer
77 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 ...
1 vote
3 answers
223 views

How do I install shapeit4 on Ubuntu/Mint?

I'm having trouble install shapeit4 4.2.2 on my new Mint 21 installation (Ubuntu 22.04 LTS). According to the official docs, the requirements are: HTSlib: A great C library for reading/writing high-...
1 vote
1 answer
65 views

Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?

I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is. I have a VCF/PLINK format file of ~8,000 individuals ...
1 vote
1 answer
174 views

Are the GIAB reference genomes (HG00N) fully phased?

Specifically, the NISTv4.2.1 HG002 dataset here (more info on Genome in a Bottle). According to their README, the HG002 v4.2.1 VCF should be fully phased. For HG001, HG002, and HG005, we have phased ...
2 votes
0 answers
129 views

Phasing genotyped data using shapeit: ERROR: Wrong ordering in physical positions

I am to phase my genotyped data with Shapeit (from ped or bed files) and I keep on getting this error message: ERROR: Wrong ordering in physical positions curr_pos=13915 prev=157299737 Any idea on ...
6 votes
1 answer
1k views

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

I have always thought that 1/0 and 0/1 in VCF genotype fields are equivalent. And yet, GATK uses both. For example, these are ...
1 vote
0 answers
58 views

How to calculate switch errors on plink formatted phased genotype data?

everyone! I'm working with haplotype inference algorithms in pedigree genotype data, and I would like to know if there is a tool or script to calculate switch errors on phased pedigree data (Plink ...
1 vote
1 answer
336 views

Interpreting imputation result from GLIMPSE

I'm following this tutorial of GLIMPSE for learning. I was expecting some extra SNPS coming from the 1000 genome reference in the resulting .vcf file. Though I understand the phasing in the output ...
0 votes
0 answers
73 views

ERROR: Failed to allocate 18446744073709551596 bytes

I'm using Eagle 2.4.1 for phasing a vcf.gz file. Whenever I give the command it gives me the following error ...
0 votes
1 answer
348 views

Tutorials on phasing and imputing low-coverage sequencing data

I am new to low-pass whole genome sequencing and have the basic idea of phasing and imputation. I have .vcf file after calling haplotypecaller tools from GATK. After searching the phasing and ...
1 vote
1 answer
72 views

Using a phased reference assembly to phase sample genotypes

I've been trying without success to phase the variants of about 30 samples in a 5Mb non-recombining region. I have a phased genome assembly of the region but so far I have not been successful in using ...
1 vote
1 answer
188 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: ...
1 vote
1 answer
70 views

Read-informed statistical phasing

I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account. I've found this paper which sounds ...
2 votes
1 answer
64 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 ...
0 votes
2 answers
74 views

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

Phasing a genome is the process of determining which variants lie on which copy of each chromosome. For example, position 5,430,500 might have an A on the paternal chromosome, but a T base on the ...
1 vote
3 answers
51 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. ...
5 votes
1 answer
405 views

Searching tool to calculate phase/switch error rate

I'm looking for a tool which, given a truth vcf file and a test vcf file, calculates the phase/switch error rate. I performed phasing of a vcf using WhatsHap and want to compare the outcome to some ...
3 votes
2 answers
282 views

Using Beagle 4.1 for phasing and IBD - chromosomes

I am trying to use beagle 4.1 for phasing and IBD analyses. I was wondering if I need to run the analysis by chromosome or I can put them together in the same vcf file.