The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.