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How do we know the stretch of variants that have been phased using haplotype caller
I am using the following command to run haplotype caller
1) I would like to know like GATK 3.6 there was an option to define active regions, is there any option in GATK v4.2.1.
2) How do we know the variants in vcf file that they are phased.
As per my understanding the symbol "|" represents hat they are phased. But which parameters that i had missed could give me information that variants starting from one position to another is phased.