Questions tagged [1000genomes]
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11
questions
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1answer
26 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 ...
1
vote
3answers
150 views
Masking sites in a vcf file
I need to mask all sites in a vcf file flagged by the 1000 Genomes Project as being unfit for population genetic analyses. The sites for all chromosomes are available at:
1000Genomes masked sites
From ...
2
votes
1answer
45 views
dbnSNP frequency anomalies
Sometimes dbSNP reports very different allele frequencies for different large-scale genome projects e.g. between 1000 Genomes and GnomAD
rs11822440 1000Genomes A=0.4629 C=0.5371 GnomAD A=0.99997 ...
3
votes
1answer
318 views
Difference between genome assembly and genome sequence alignment to a reference to find structural variants
I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations.
I've been ...
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0answers
11 views
Difference between "trans-ethnic" and "cross-ancestry"
A quick terminology question today. I see the terms "cross-ancestry" and "trans-ethnic" used seemingly interchangeably in literature. Is there any real difference between those two ...
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votes
2answers
127 views
Removing common variants in the 1000 genomes database from .vcf [closed]
I have 15 .vcf files. I need to remove `common variants in the 1000 genomes database' appearing in at least 0.5% of the population
Do you know from where I may start?
Thank you so much
0
votes
1answer
58 views
Obtaining HGDP project data in fasta format
I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes....
1
vote
1answer
101 views
There's a faster way to download 1000 Genomes phase 3?
I'm trying to download the 1000 Genomes (phase 3) through FTP, but it's taking ages.
I saw the documentation about using Aspera (fasp protocol), but the instructions don't work: ...
0
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1answer
140 views
Simulating phenotype with the 1000 Genomes Project
I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation?
I'm trying to use ...
1
vote
2answers
79 views
1000 genomes missing SNPs on chr X in GRCh38
I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant ...
0
votes
1answer
128 views
what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays?
About 5 years or so ago, it used to be the latest release of the CSHL ...
