7
$\begingroup$

I have the genotyped data from impute2 output in .gen format (imputed to 1000G P3). The file has genotype posterior probabilities (GP:3 values per variant). I have converted .gen to .vcf using qctools and the .vcf file has GT:GP format. I need to convert the .vcf file with GT:GP format to GT:DS. Genotype dosages are recommended for use in qtltools/fastqtl analysis. However, I cannot find a tool that would keep the .vcf format and convert GP to DS. Any help much appreciated!

$\endgroup$
5
$\begingroup$

You can do this in Hail.

Here's the rough code to do it (0.1 versions).

Setup:

from hail import *
hc = HailContext()

Import the .gen file. VCF works too:

dataset = hc.import_gen(
    'src/test/resources/example.gen', 
    'src/test/resources/example.sample')

Remap the genotype schema and export to VCF:

dataset.annotate_genotypes_expr('g = {GT: g.call(), DS: g.dosage()}')\
    .export_vcf('/tmp/out.vcf.bgz')

Take a look at the getting started page if you want to try it out!

I should note that you may be able to do QTL analyses in Hail, depending on the method you want to use. See blog post here.

$\endgroup$
2
$\begingroup$

Hm, I didn't know that the plugin existed so I wrote my own script to convert GP to minor allele dosage on github. Maybe someone else will find it useful :) https://github.com/7methylg/VCF-GP-to-DS

$\endgroup$
0
$\begingroup$

There's the dosage plugin for bcftools, but it only outputs tab separated values. It would not be too hard to extend the plugin to output a VCF with the DS tag instead, but it has not been done yet. There's a good chance the bcftools devs would respond to a feature request...

In any case, this code:

curl https://raw.githubusercontent.com/samtools/bcftools/develop/test/convert.vcf > convert.vcf
bcftools +dosage convert.vcf > output.tsv
head -2 output.tsv 

has the output:

#[1]CHROM       [2]POS  [3]REF  [4]ALT  [5]NA00001      [6]NA00002      [7]NA00003      [8]NA00004      [9]NA00005      [10]NA00006     [11]NA00007     [12]NA00008    [13]NA00009     [14]NA00010
X       2698560 G       A       0.1     0.0     0.1     0.2     0.3     0.2     0.2     0.2     0.2     0.1

This is using bcftools version 1.3.1.

Here is an excerpt from the bcftools manual for the dosage plugin:

dosage

print genotype dosage. By default the plugin searches for PL, GL and GT, in that order.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

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