Could anyone explain me a little bit these two lines of my GVCF file ?
Why I'm getting "NON REF" alternative allele? And why for the second line I only see END information and not the rest?
GL000192.1 546636 . G A,<NON_REF> 49.77 . BaseQRankSum=1.026;ClippingRankSum=1.026;DP=4;MLEAC=1,0;MLEAF=0.500,0.00;MQ=49.02;MQ0=0;MQRankSum=-1.026;ReadPosRankSum=0.000 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:2,2,0:4:78:0|1:546636_G_A:78,0,87,84,93,177:1,1,1,1
GL000192.1 546637 . G <NON_REF> . . END=546645 GT:DP:GQ:MIN_DP:PL 0/0:4:11:4:0,12,99
I know that NON_REF represents any possible alternative allele at this location, but if my genotype is 0/0 (homozygous for reference)... this line makes no sense for me.
Thanks in advance.