Test-drive the GATK tools and Best Practices pipelines on Terra
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weird lines when calling variants with GATK, this might be a common issue
I called variants and some lines are weird in the output g.vcf file
chr05 9723222 . A C, 1013.03 . DP=21;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=61996,21 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:0,21,0:21:69:0|1:9723222_A_C:1027,69,0,1027,69,1027:9723222:0,0,15,6
The weird part is in bold format. Did anyone get the same problem as me?