how to get coverage information from the 1000 genomes data

[kjaja]

Hi All,

What is the best way to check if a variant at a specific location is well covered in the 1000 genomes. The way that I am pulling this information is by slicing the bam files and viewing the reads in IGV. Is this information summarized for all the samples in the 1000 genomes project?

thanks

[laura]

For what purpose do you want the coverage info?

[kjaja]

when filtering out variants in the 1000 genomes, I am left with variants that were not filterd out becuase the region was not well covered in the 1000 genomes.

[laura]

You should be able to look at the genotype likelihood values to give you similar information. If all three genotypes have the same likelihood this means the genotype was imputed and the coverage is zero, you will have to look at each individual but this will be easier than getting the depth for each site from each individual from each bam file