I'm getting the output from GATK
ChrSy 198904 . C . 44.99 LowQual AN=2;DP=8;MQ=39.35;MQ0=0 GT:DP 0/0:8
ChrSy 198904 . CGTCCGATATTTGCGAAATATCG . Infinity . DP=8;MQ=39.35;MQ0=0 GT ./.
ChrSy 464065 . A . 113.99 . AN=2;DP=37;MQ=25.38;MQ0=0 GT:DP 0/0:37
ChrSy 464066 . G . 113.99 . AN=2;DP=37;MQ=25.38;MQ0=0 GT:DP 0/0:37
ChrSy 464066 . GTT . 60.03 . AN=2;DP=37;MQ=25.38;MQ0=0 GT:DP 0/0:28
ChrSy 464069 . T . 113.99 . AN=2;DP=37;MQ=25.38;MQ0=0 GT:DP 0/0:37
Why do positions 198904 and 464066 have multiple-base REF but ALT="."? Why did GATK merge them in
a single line unlike other positions_(emit-all sites VCF)_ and still have a duplicated position preceding it?
I thought only indel has an anchor base(position before the event)?
Does ./. mean "same with the reference"?
Thank you!
