Question: How to get bi-allele genotype data from 1000 genome project for African population
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gravatar for AHW
9 months ago by
AHW40
India
AHW40 wrote:

I am trying to get bi-allele genotype data from the 1000 genome project for the African populations. It would be great if anyone can take me to the link.

genome • 232 views
ADD COMMENTlink modified 9 months ago by Kevin Blighe66k • written 9 months ago by AHW40
1
gravatar for Kevin Blighe
9 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

If you follow steps #1 and #2 here, then you will have all of the information that you require: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

Note that the files are large and are split by chromosome.

Once you have downloaded everything, my recommendation would be to obtain the IDs of the African samples from the downloaded PED file, and then filter each chromosome BCF for just these samples.

Also note that these are GRCh37 co-ordinates.

Kevin

ADD COMMENTlink modified 9 months ago • written 9 months ago by Kevin Blighe66k

Thank you so much for your comments. I got the data for the specific African populations and my data looks like

 CHROM       POS         ID REF ALT QUAL FILTER                                                                                                                                                                        INFO HG02943 HG03100 NA19023 HG03078 HG03085 HG02464 HG02574
    1   4131726  rs3936238   A   G  100   PASS                                                AA=A|||;AC=4;AF=0.409345;AFR_AF=0.3343;AMR_AF=0.4308;AN=14;DP=23035;EAS_AF=0.3294;EUR_AF=0.5497;NS=2504;SAS_AF=0.4335;VT=SNP     0|0     0|0     1|1     0|0     0|1     0|0     1|0

NS=2504 shows the sample number, how can I get the data for all these individuals.

ADD REPLYlink modified 9 months ago • written 9 months ago by AHW40
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