Can I get SNP information by individual from dbSNP

Question

[Chen Sun]

Hi all,

I download the dbSNP data, both all and common SNP information, which is produced by 1000G project.

But I do not want to use all the information. I want to use just one individual's SNP information, but I did not find the relation between each SNP ID and individual ID.

Is there a way I can extract or acquire just one individual's SNP information for analysis?

Answer 1

[Chen Sun]

For those who concerned, there is a website that can get at least Venter's SNP information, please refer to this: http://huref.jcvi.org/

Answer 2

[Pierre Lindenbaum]

For a VCF use bcftools with option

-s, --samples [^]LIST

Comma-separated list of samples to include or exclude if prefixed with "^".

-S, --samples-file [^]FILE

File of sample names to include or exclude if prefixed with "^". One sample per line. The command bcftools call accepts an optional second column indicating ploidy (0, 1 or 2) and can parse also PED files. With bcftools call -C trio, PED file is expected.

[Jimbou]

The Impute2 website offers phased haplotype files of the 1000G samples:

https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference

[Chen Sun]

I mean, all I get is mixed SNP information, there is no column indicate which individual it come from