Supplementary aligments in VAF

Question

[deniselavezzari]

Hi everyone! I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot,

[ATpoint]

It is good practice to indicate crossposts between communities: https://bioinformatics.stackexchange.com/questions/15352/supplementary-aligments-in-vaf

[ATpoint]

As for the question, I'd say that it depends on whether the variant caller that was used in the first place did consider these alignments or not. If considered then yes, count them. If not then not. You would probably need to refer to the manual of the variant caller to find that out.

[deniselavezzari]

Thanks, I was wondering if there is a "general rule" indipendent from the variant calling.