1000 Genome ,Dbsnp132 ,Hap Map Frequency For A Set Of Variant

Question

[Abdel]

Hi everybody

I have a large set of variant , i have to get allele frequency of CEU,YRI and JPT populations from 1000 genome , dbsnp132 and hapmap .

I simply don't know where to begin....should I download all 1000 genome ,dbsnp and HAPMAP database ?

what files should I download ? there is lot of downloadable data and i don't know what to download . I'm using perl to parse data generally , do anyone can explain me exactly what i should do ?

Thank you to be patient with me ,I'm novice

[Pierre Lindenbaum]

Abdel, 4 of your 6 questions have already been answered on this site. Please, validate the correct answers. e.g: A: Chromosome Position In The Ucsc Phylop46Way.Placental.Wigfix File

Answer 1

[Jorge Amigo]

some of the questions you post here have been already discussed in this forum, hence you will gain a lot of experience if you try performing different queries on BioStar regarding all the issues you arise: 1000 genomes, dbSNP, HapMap, download and parse locally or query remotely, ...

in case it helps in any way, just trying to save you some time, you are able to get allele frequencies for your populations of interest through SPSmart (disclaimer: I am the main developer), since it has been built to facilitate this kind of simple bulk queries for population genetics purposes. it does cover the latest releases of 1000 genomes and HapMap, but unfortunately it doesn't contain dbSNP frequencies.

[Abdel]

It seems like a really powerfull tool , i'm interested on the stand alone version , it take a lot of time to prepare all the stuff , but i'll try it...i was wondering if it works with novel variant (no rs) ?

[Jorge Amigo]

yes, you can provide chromosome positions, and if they match 1000 genomes variants positions it will report their full stats.

[Abdel]

Thanks Jorge that was helpfull

[Htn]

Hi Jorge, Why there are only 68 CHB samples (1000 Genomes) on SNPsmart?

[Jorge Amigo]

the data summarized on SPSmart from the 1000 genomes project comes from the Phase I interym analysis they released, in which only 68 CHB samples were sequenced.

[Htn]

Ah, Thanks Jorge! Now, there are 97 samples (low coverage).

[Jorge Amigo]

we need to work with raw genotypes in order to provide all the population statistics SPSmart has, and for that reason we can only work with bulk data when it is frozen and released. we do not want to compete (nor would we be able) with 1000 genomes data interface which gets updated constantly as new sequenced data is available, but to complement it.