Variant calling tutorial

In this tutorial, you will be using DeepVariant on the Galaxy platform for calling SNVs in a SARS-CoV-2 genomic sample followed by variant annotation using snpEff.

The test dataset for this exercise was obtained by downsampling SARS-CoV-2 sequence data from ENA browser. You can download the downsampled BAM file (and its index) and the NC_045512.2 reference sequence (and its index) for download below.

Use the comments area to discuss the following questions:

1) Why are all the SARS-CoV-2 variants genotyped as homozygous in the output VCF from DeepVariant?

2) What are the differences between the VCF outputs from DeepVariant and snpEff?

3) How many missense variants are in the test SARS-CoV-2 sample?

4) How many disruptive in-frame indels are in the test SARS-CoV-2 sample?