Questions tagged [phasing]
The phasing tag has no usage guidance.
13
questions
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1answer
28 views
Interpreting imputation result from GLIMPSE
I'm new to the imputation and phasing. 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 ...
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0answers
56 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
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0
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1answer
63 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 ...
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0answers
31 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 ...
1
vote
1answer
46 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
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1answer
47 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:
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0
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1answer
44 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 ...
2
votes
1answer
54 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 ...
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2answers
54 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
1answer
67 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 ...
1
vote
3answers
48 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
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1answer
229 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 ...
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2answers
155 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.
