2
votes
1answer
208 views

Ancestral Allele explanation

I'm having some trouble understanding the concept of ancestral allele. What exactly does it mean? What does it have to do with Identity by descent/state? What does it have to do(if anything) with ...
3
votes
3answers
101 views

How do you merge SNP data with a reference genome?

My Data I have a 23andMe file listing SNPs in the form: ...
3
votes
3answers
65 views

Publicly available genotype data?

I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this: ...
2
votes
1answer
54 views

Could someone clearly define what a gene variant is with an example

Could someone clearly define what a gene variant is with an example. I am totally confusing myself with SNPs, alleles, variants and how the major and minor allele are defined. A clear example with ...
0
votes
1answer
433 views

What is the difference between SNP and STR?

I thought that these were just different format of the same data. But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right? ...
5
votes
1answer
55 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
1
vote
1answer
325 views

How to compare SNP from genotyping results for multiple people with a known phenotype?

I'm looking at different genotyping profiles available at opensnp.org and am trying to compare profiles for people with different phenotypes. For example, given 10 profiles of people who can roll ...
4
votes
3answers
101 views

Is there any source for raw data of SNP genotype frequency?

On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares ...
1
vote
1answer
199 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...