Exporting a subset of variants

[Richard Kerr]

Just started using msprime and it seems real fast!

My problem is that I am relatively new to Python and writing code isn't coming all that easy.

Someone mentioned in the past that to get a dataset that fits the bill you should aim to get more SNPs than you need, and then randomly subsample.

Can anyone advise me on the most efficient way to sample a subset of the SNP? I have successfully called msprime.simulate and have the tree sequence object at hand.

Ultimately I would like to write the genotypes out using write_vcf(), but only write out the subsample. Not sure if this is possible.

Any help would be greatly appreciated.

Richard

University of Tasmania, Australia

[Jerome Kelleher]

Hi Richard,

The best way is to subset the sites like you've been doing in your other
email, and then call write_vcf() on the subsetted tree sequence.

Cheers,
Jerome

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