4
votes
what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
The best set I'm aware of can be downloaded from https://gnomad.broadinstitute.org .
4
votes
Difference between genome assembly and genome sequence alignment to a reference to find structural variants
the first being what the 1KGP and SDGP did and sequence the whole
genome, align the reads to the reference genome and end up with a BAM
file.
If you have a well defined reference genome (e.g. human, ...
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4
votes
Accepted
Removing common variants in the 1000 genomes database from .vcf
Use VEP, ANNOVAR or snpEff to annotate your VCF file (I'd recommend combining your VCFs into a single file if they're single sample VCFs or are all comprised of samples from the same experiment/cohort)...
- 2,086
3
votes
Accepted
1000 genomes missing SNPs on chr X in GRCh38
As I told you on 1000 genomes helpdesk:
Because of the ploidy settings we used for our variant calling, we only called variants in the the pseudoautosomal region on the X chromosome. We are working on ...
- 1,749
3
votes
Interpreting short indel calls in 1000 Genomes Project VCFs
Older GATK was using the so-called variant model where overlapping variants were combined during calling. More recent GATK is using the allelic model where one non-reference allele is evaluated at a ...
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2
votes
Accepted
Interpreting imputation result from GLIMPSE
It seems that you didn't use the following flag:
...
- 1,679
2
votes
Masking sites in a vcf file
I've tried many ways to do this with bcftools but don't think it's possible to exclude a bed file. What you want is
...
- 152
2
votes
Accepted
Where can I download 30x 1000 genomes cram files?
Yes, those are the .cram files for the 30x whole genome sequencing data for 1000 genomes.
If you want 10x and 30x sequence data for the same individual, you can just downsample the 30x .cram file ...
- 1,679
2
votes
1000 genomes missing SNPs on chr X in GRCh38
I think these are biallelic snps:
The set is restricted to biallelic SNVs and INDELs.
If you check the liftover version, the chromosome X is complete...
- 1,678
2
votes
Accepted
Interpreting short indel calls in 1000 Genomes Project VCFs
this is Marta from the NYGC. Thanks for reaching out with your questions.
The full SNV/INDEL callset that we released (listed as "SNV/INDEL VCFs" in the key resource table in our paper) ...
2
votes
LD clump GRCh38 GWAS results
Is 1kg.v3.tgz based on GRCh37?
Is there a GRCh38 reference version of 1000 genomes that is split to different super populations (EUR etc)?
Yes, the genome build for 1000 Genomes phase 3 release is ...
1
vote
Should genotype imputation be ancestry specific?
Basically, yes, you will get better results if you use a reference panel which contains samples with similar ancestry to your targets. Imputation works by matching haplotypes in your target samples to ...
- 1,679
1
vote
Where do I get a large reference VCF?
For anyone who arrives here looking for a large reference VCF but not wanting GRCh37, you might consider the HGDP+1KG subset of the Genome Aggregation Database's dataset. You can find a VCF file per ...
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1
vote
Accepted
Where do I get a large reference VCF?
Solution: Use https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/, then to get the ancestry information (i.e., the ancestry group of each sample, e.g., "HG00566"...
- 513
1
vote
Interpreting short indel calls in 1000 Genomes Project VCFs
Often multi-allelic sites would be split into several lines (one per alternate allele) to make filtering easier for specific types of alternate alleles (e.g. filter out MNV vs SNV).
VCF-level, one ...
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1
vote
Accepted
Chosing an imputation panel for SNP-Chip data?
If you're using an hmm-based method such as for example impute2 or later, then the imputation method will perform the haplotype matching for you. No need to cut down the reference panel. Try to get a ...
- 2,236
1
vote
Chosing an imputation panel for SNP-Chip data?
If I were you, I would use ADMIXTURE in supervised mode --supervised and use some of the 1000 genomes populations as reference populations. This is a fast and ...
- 1,679
1
vote
Masking sites in a vcf file
If you are familiar with Python, check out the pyvcf.VcfFrame.filter_bed() method I wrote:
...
1
vote
dbnSNP frequency anomalies
I'll stick my neck out and simply state that allopatry alone would account for the pattern you are observing. Thus populations can exihibit variation in allelic profiles, particularly where Mendellian ...
M__♦
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1
vote
Simulating phenotype with the 1000 Genomes Project
You might try ldscsim which was developed by Nik Baya for this purpose.
https://hail.is/docs/0.2/experimental/ldscsim.html
...
- 241
1
vote
Accepted
Simulating phenotype with the 1000 Genomes Project
I managed to get it done without the gcta64.
I have written a Jupyter Notebook with the steps: https://github.com/bambrozio/bioinformatics/blob/master/utils/1k-genomes-phenotype-simulator.ipynb
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