3
votes
What tool I can use to map short-reads sequences to reference genome and get specific mapped size
If you have a SNP panel then you have the coordinates on the genome. You can use tools such as bedtools slop to expand the coordinates to the desired length and then extract those regions from the ...
- 156
2
votes
Getting VCF file that contain common SNPs from 6 VCF file using isec
You've used the right tool and gotten the right results. What you need to understand is that VCF contains variant loci as well as the genotypes for >=1 sample(s) at those loci. The intersect ...
- 1,744
2
votes
When it is stated in your consumer genetics testing report that you have x% (lets say 1.3 percent...) Neanderthal DNA, what is actually meant?
Based on reading a similar post it seems like if the report says I am 1.3 percent Neanderthal then it does NOT mean 1.3% of my base pairs or SNPs of my genome (or exons or protein coding region or ...
2
votes
When it is stated in your consumer genetics testing report that you have x% (lets say 1.3 percent...) Neanderthal DNA, what is actually meant?
I ran a basic search of 23andme and it looks like they use known variant loci from the Neanderthal genome. Also, they expect a 2-2.5% overlap. See:
https://customercare.23andme.com/hc/en-us/articles/...
- 1,744
2
votes
Getting nearest gene from SNP data using SNP ID, CHR, and BP
This answer assumes that you have a terminal that runs linux commands and python, and that you can install and run bedtools.
step 1: convert your input spreadsheet to BED format.
There is probably an ...
- 3,409
2
votes
Retrieve rsIDs from chromosome positions using MRutils::get_rsid_from_position
An alternative possibility in R is using the library biomaRt from Bioconductor. Here an example starting from a table with 3 columns: Chr, Start, End. Organism is human and positions are assumed to be ...
- 705
2
votes
Accepted
VCF: false insertions?
Microsatellites, minisatellites and other type of repetitive variation are a known feature of genomes.
I agree with previous comments in the sense that what you are observing here might as well be ...
- 705
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
...
- 221
1
vote
Maintaining SNP names when calculating allele frequencies from a VCF file on plink 1.9
The standard and most common way to name SNPs is by using rsIDs.
The reason your output from PLINK does not include SNP names is because these are not included in the original VCF you are working with....
- 705
1
vote
Can you infer orientation from vcf file data?
SNPedia introduces its own orientation to cut the tie to a reference genome, such that the bulk data is independent of the reference genome in use. The intention is good. The implementation is ok. It ...
- 6,295
1
vote
Can you infer orientation from vcf file data?
To answer (a small) part of my own question 'Why is AA not the same as TT in this case?' - I believe the answer to this is that the flanking sequence is important here. We can't just flip an AA to a ...
- 131
1
vote
Can you infer orientation from vcf file data?
SNPedia seems to show transcript base change and not genomic base change, so their C>T is the same as the G>A you note.
I don't understand SNPedia's allele notations completely, other sources ...
- 1,744
1
vote
Variants list to aminoacids
Neither C1092T nor OPG001:D162N seem to follow HGVS conventions. You could try to convert them to HGVS nomenclature standards ...
- 1,744
1
vote
Accepted
Converting a Dante Lab VCF file
If your file doesn't contain the rsIDs, you can use a tool like Ensembl's VEP to annotate the file and get rsIDs as well. Of course, not all variants have an rsID so don't expect to find one for ...
- 9,352
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