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Test-drive the GATK tools and Best Practices pipelines on Terra
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A question about a weird output of VCF file from UnitedGenotyper
When I call variants using UnitedGenotyper, usually, the 9th column of a vcf file would be GT:AD:DP:GQ:PL and it indicate the information that the following columns have. But when I called variants using --output_mode EMIT_ALL_SITES, the output of VCF file is a little bit different as following:
chr1 4091284 . T . 57.60 . AN=6;DP=92;MQ=69.06;MQ0=0 GT:DP 0/0:69 0/0:14 0/0:9
The ninth column only contains GT and DP. But I also want to know the number of reads covering reference alleles and the number of reads covering alternative alleles. Although there are a few rows are normal, most of the rows are lack of information.
Can I ask how I can get all the information I need? Thanks.