Individual or joint variant call ing

Question

[priya.bmg]

Hello

I need a suggestion. I have exome data of 6 subjects. As the sample size is very less, should we do variant calling on every sample (https://gatk.broadinstitute.org/hc/en-us/articles/360037226672-CNNScoreVariants) rather than joint variant calling?.

P.S These 6 subjects belong to same generation or a different generation in a family with common ancestor.

Thanks

Priya

[brunobsouzaa]

Personally, I prefer performing variant call on every sample. But doing joint genotyping is also valid... So, see what best fit your purposes!