Question
Question Posted 08/02/19:
Hi，ADNI, I will explain my questions with the following example:
eg: In merged GATK vcf data of ID 141_S_4232, the ref is T, but there was three alt variants at chr3 119552561(C,TCC,TC), and the GT is 0/3, while in VASACA vcf data of the same position of the same person, the ref value is T,and the alt is C, the GT is 0/1.
My first question is what does GT=0/3 mean in merge GATK vcf data? Does it mean T>TC mutation? If yes, why the result is different between GATK and VASACA vcf data? The last question where could I download the GATK vcf for singe sample?
Hi，ADNI, I will explain my questions with the following example:
eg: In merged GATK vcf data of ID 141_S_4232, the ref is T, but there was three alt variants at chr3 119552561(C,TCC,TC), and the GT is 0/3, while in VASACA vcf data of the same position of the same person, the ref value is T,and the alt is C, the GT is 0/1.
My first question is what does GT=0/3 mean in merge GATK vcf data? Does it mean T>TC mutation? If yes, why the result is different between GATK and VASACA vcf data? The last question where could I download the GATK vcf for singe sample?
Response posted 08/07/19 by Kwangsik Nho:
Please use GATK vcf files, which are more accurate than CASAVA vcf files.
