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missing AD after selectVariants from HaplotypeCaller joint variant calling

Hello!

I called variants for a trio using HaplotypeCaller cohort pipeline. Since I need to do quality control on individual samples, I used SelectVariants to parse out variants for each individual. The process ran without crash/warning. However, I found most of variants are missing AD information in the "Sample" column (last column in VCF file), even some missing DP. However, those informations are in the original joint variant calling VCF file. Is there any way to recover this or this is the way? Could you also tell me the reason for this?

thanks,

Ying

Answers

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