User: moxu

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moxu470
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Posts by moxu

<prev • 216 results • page 1 of 22 • next >
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How Did 1000 Genomes Project Enroll Samples To Populations
... When 1000 Genomes Project enrolled a sample to a population (e.g. CHB or LWK), what criteria did they use to ensure the individual really belongs to the underlying population? Did they require something like, to qualify for a LWK sample, 8 of your great grandparents have to only lived in where whate ...
genomes population written 5 months ago by moxu470
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How to build an imputation reference panel from a fasta file of many samples
... I have a fasta file for dozens of thousands of human mitochondrial genome sequences (aligned already) in fasta format. I want to construct a reference panel using these samples to impute genotyped samples, but I don't know how to do so properly. BTW, anyone has thought about how to impute mtDNA mar ...
assembly alignment snp sequencing written 18 months ago by moxu470
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Comment: C: How to plot haplogroup map with pie charts?
... Have you found a solution? Given a haplogroup, how do you find our the geographic information associated with the haplogroup? ...
written 20 months ago by moxu470
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Comment: C: Y-DNA and mtDNA Haplogroup Predictor
... Thanks so much for the reply. How about MToolBox? ...
written 20 months ago by moxu470
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Answer: A: Y-DNA and mtDNA Haplogroup Predictor
... I am looking for a good haplogroup classifier using either genotyped information (SNPs) or WGS information (sequencing). Which software products are the most popular (and accurate)? Thanks! ...
written 20 months ago by moxu470
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Comment: A: Plot local ancestry on chromosome
... Any luck? It looks like Martin's approach is outdated. ...
written 24 months ago by moxu470
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Comment: C: How plink calculates the INFO scores ?
... Have you got an answer? ...
written 2.2 years ago by moxu470
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Answer: A: How to convert Merlin phased result files to vcf
... The answer is that mega2 cannot take Merlin's .chr/.flow as input and cannot convert them to .vcf. The suggestion I got from the mega2 professor is to use shapeit, which can do trio phasing and can convert to vcf. ...
written 2.3 years ago by moxu470
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How to convert Merlin phased result files to vcf
... I used Merlin to do family trio phasing. Merlin generated a .chr file and a .flow file for each chromosome. I need to convert these files to .vcf files, or at least to a format that is more modern and popular. Any suggestions/recommendations would be highly appreciated. ...
genome assembly snp software error written 2.3 years ago by moxu470
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How to resolve kinship with the software "king" using GWAS genotyping data?
... "king" can impute IBS0 and kinship coefficient using GWAS samples. It can generate Z0 (probability of IBD0) for within-family members but this is not common for a GWAS population. So how can you resolve the kinship using the king output file? For instance, how can you tell parent-child, monozygotic ...
snp written 2.4 years ago by moxu470

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