1000Genomes YRI trio, NCBI36/37, rs334

[raonyguimaraes]

Hello all!

I was asked to download the data of a trio of YRI from the 1000genomes Project. So I looked at all the data published by the project and I found a release with the file above that had the data I needed for my analysis.

ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz

This data comes mapped for the build NCBI36 so I used the liftover tool from UCSC to convert the coordinates for the build NCBI37.

So far so good, but then comes my two dilemmas:

1) I was asked not to convert the data from NCBI36 -> NCBI37 and I was given advice to look for an already published version of this trio data for the build NCBI37, so my first question is if someone know if such data exists or not cause I couldn't find.

2) For this trio of YRI, there are 4502439 snps but we are especially interested in the SNP rs334 that should be at the chromosome 11 at 5204808 for NCBI37 or 5204808 for NCBI36. This SNP is responsible for the sickle cell disease and I couldn’t find this SNP on this data. This SNP should be common specially for the YRI population so I would like to know why I’m not finding this SNP in this genome trio.

I hope someone will have some clue about those questions. I would appreciate some feedback from the community.

[Jim Robinson]

Hi, I looked at the alignments for this site in IGV and it indeed looks like the snp is there in the father and daughter as a het, but not the mother. Also I can confirm it does not appear to have been called. Perhaps this is a false-negative, they do occur.

You can look at this yourself without downloading any BAM files by (1) start IGV, (2) select "File > Load from Server and open 1000 Genomes > Pilot YRI Trio. Then select one or more bams.

I don't think you'll find this published for b37.

Here's a screenshot