How does the LeftAlignAndTrimVariants with --splitMultiallelics tool affects the AC, AF, AN fields and also if multiple alleles are split then on what basis it splits the PL field which helps to determine the genotype.
All the fields should be split by allele, unless you request --keepOriginalAC. Can you post an example record you are asking about?
Here is one example. I have used LeftAlignAndTrimVariants with --splitMultiallelics, now how does GATK determines in PL value and decides the genotype for second allele ?
chrI 409 . G A,T 98 . DP=31;VDB=5.556450e-02;AF1=1;AC1=2;DP4=0,0,29,2;MQ=20;FQ=-105 GT:PL:GQ 1/1:131,78,0,111,6,95:99
LeftAlignAndTrimVariants with --splitMultiallelics tool
chrI 409 . G A 98 . AC=2;AF=1.00;AN=2; GT:GQ:PL 1/1:99:131,78,0
chrI 409 . G T 98 . AC=0;AF=0.00;AN=2; GT:GQ:PL 0/0:99:36,16,0
Interesting. That is unexpected. Is that the entire record for the site before splitting? How did you produce the VCF? Are you using the latest version of GATK?