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why the vcf generated by gatk1.4.1 is different from the old ones?
I followed the best practice pipeline using the gatk4.1.4 and generated the final recalibrated vcf file. However, this file is quite different from the public available vcf in format (eg. the QUAL value is normally much larger in my vcf). Is this expected because of using different versions of gatk? How to combine these two to perform GWAS analysis?
Please find the attached files for details.
Your help is much appreciated!