Cannot download hail.utils.get_1kg('data/')


#1

when i run the command for download, the web speed is too slow and i cannot download anything. Do anyone have the data‘s web link for download? Thanks so much for your help!!!


#3

You will need two files:

Are you using a cluster or a single computer? If you are using a cluster, ensure these two files are in HDFS or in another filesystem that is readable by the entire cluster.

To convert the compressed VCF file into a Hail Matrix Table (and save it on disk), execute this:

import hail as hl

imported = hl.import_vcf('/path/to/1kg.vcf.bgz', min_partitions=16)
imported.write('/some/other/path/1kg.mt, overwrite=True)

In the notebook, you must replace

mt = hl.read_matrix_table('data/1kg.mt')

with:

mt = hl.read_matrix_table('/some/other/path/1kg.mt')

You also must replace the path to 1kg_annotations.txt here:

table = (hl.import_table('data/1kg_annotations.txt', impute=True)
         .key_by('Sample'))

#4

Thanks! I have downloaded the data by your links and commands:smile::smile::smile: