Can I use joint calling on a custom target capture gene panel for detection of germline mutations?

Hello, I have a batch of 190 germline target capture samples prepared covering a gene panel of about 7Mb. I am just wondering if I can use GATK joint calling and what would be the minimum sample size requirement.

From github.com/gatk-workflows/gatk4-germline-snps-indels, the workflow recommends at least 1 WGS or 30 Exome samples while gene panel is not recommended.

What is the recommended best practice for this scenario? Shall I use individual variant calling instead?

Thanks a lot in advance!
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  • nelsonobhknelsonobhk Member
    Thank you SkyWarrior! I will do do joint genotyping then.

    Is it true that VQSR cannot be applied in my scenario and I can only perform hard filtering? Thank you once again!
  • nelsonobhknelsonobhk Member
    That's a very good suggestion, I shall try it out. Thank you!
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