high depth Illumina samples from 1000 Genomes

Question

[Floydian_slip]

Hi,

Is there a way to batch download alignments from only high depth samples that were sequenced using Illumina from the 1000 Genomes site? Phase (pilot, 1, 2 or 3) is not important. I am looking for atleast 30X. I see that there were samples in the pilot phase that were 50X.

Thanks,

~N

Answer 1

[Chris Fields]

The BAM files are available from several locations including NCBI and EBI, though you'll need to sort out the low and high coverage ones:

http://www.1000genomes.org/category/bam

Summary data for the pilots:

http://www.1000genomes.org/data

[Floydian_slip]

Thanks Chris,

Is there a quick way to identify some samples that have high coverage since clicking each sample will take a long time. I tried to find a spreadsheet or a table that lists the samples along with their coverage but could not find it.

Thanks again!

[Chris Fields]

The second link about has information (including a link to an Excel spreadsheet with all the info). The pilot data has a number of high coverage runs, such as NA12878.