2
$\begingroup$

I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to retain the confidence of base calls? Can GATK be used to analyse this data?

$\endgroup$

1 Answer 1

2
$\begingroup$

This is a good idea - low pass sequencing has shown to be better than genotype arrays for things such as GWAS or QTL mapping.

The primary way of processing low-pass sequencing data is to use imputation - partciularly methods such as GLIMPSE or QUILT and a large reference panel such as the HRC or TopMed in order to refine the genotype calls.

This is a figure from the GLIMPSE paper showing how you can retain variants of different frequencies at different levels of sequencing depth.

enter image description here

And a similar image from the QUILT paper:

enter image description here

You might also want to check out some of the methodology in this paper http://m.genome.cshlp.org/content/31/4/529

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.