Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.