Say I have two VCFs with 100 samples in each file. Each VCF was joint-called separately and now I want to merge the variant calls.
Do I need to left-align the INDELs in the merged VCF? I've used
bcftools norm in the past and got odd results. It seems that
vt is a better tool for this.
Is left-aligning only useful for common variants? If I'm interested in rare variants (<0.5% AF) would left-alignment actually matter?
Here's an example of bcftools norm
chr7 157009949 . AGCGGCGGCGGCG AGCGGCGGCGGCGGCGGCG,A,AGCGGCGGCGGCGGCGGCGGCG,AGCGGCGGCG,AGCGGCGGCGGCGGCGGCGGCGGCG,AGCGGCGGCGGCGGCG
Left-Aligned VCF (with multiallelics split into biallelic calls)
chr7 157009949 . A AGCGGCGGCG chr7 157009949 . A AGCGGCGGCGGCG chr7 157009949 . A AGCGGCG chr7 157009949 . A AGCG chr7 157009949 . A AGCGGCGGCGGCGGCG chr7 157009949 . AGCG A chr7 157009949 . AGCGGCG A chr7 157009949 . AGCGGCGGCGGCG A