True variants selection

Question

[maevalefeuvre]

Hello,

Is it important to filter variants based on the Allele Count in genotypes for each ALT allele (INFO/AC)? Should I always, by default, set this value to a minimum of 1 (using bcftools -c1) in order to filter for true variants?

thank you :)

[Pierre Lindenbaum]

well that's a start, if AC=0 there would be no variation...

[maevalefeuvre]

thank you , So, if AC=0, should I discontinue the analysis, or is there another parameter I can check even though AC=0?

[dthorbur]

All annotations can be useful in filtering, depending on your goals. So yes, AC can be useful, but there is no rule on setting thresholds. It depends on data, how you called variants, goals, etc... Here is a tutorial from the GATK team on hard filtering which may be useful.