Improve coverage in callvariants.sh

Question

[Hayler Edu]

Hello everyone

I do variants calling using bbtools (callvariants.sh) but the coverage of the SNPs was too small.

Does someone know if that is possible to improve the coverage?

I need SNPs with coverage=10

Answer 1

[GenoMax]

You can't "improve" coverage if you do not have enough reads in your dataset that are aligned. You will need to sequence more, assuming your data alignments have worked without any problems.