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 .
Christopher Chang's user avatar
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, ...
Chris_Rands's user avatar
  • 3,948
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)...
Ram RS's user avatar
  • 2,310
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 ...
Emily_Ensembl's user avatar
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 ...
user172818's user avatar
  • 6,515
2 votes
Accepted

Interpreting imputation result from GLIMPSE

It seems that you didn't use the following flag: ...
user438383's user avatar
  • 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 ...
pgcudahy's user avatar
  • 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 ...
user438383's user avatar
  • 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...
StupidWolf's user avatar
  • 1,688
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) ...
Marta Byrska-Bishop's user avatar
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 ...
Lloyd_LiuSiyi's user avatar
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 ...
user438383's user avatar
  • 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 ...
Daniel King's user avatar
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"...
BigMistake's user avatar
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 ...
JRodrigoF's user avatar
  • 827
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 ...
winni2k's user avatar
  • 2,266
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 ...
user438383's user avatar
  • 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: ...
Seung-been Steven Lee's user avatar
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__'s user avatar
  • 12.3k
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 ...
Daniel King's user avatar
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
Bruno Ambrozio's user avatar

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