I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its arguments (--max_alternate_alleles 1) and 2 in second. Output was different by number of 600 SNVs,
a) There are sites on which haplotype caller for second command changed SNV on the one with better scores than in first command. eg. CSB10A_v1_contig_682 232 ref.: G first: GT(90.75) second: GTT ( 135.73). Scores in brackets.
b) There are sites where unlike first command, second command didn't give any SNVs, because there was no mapped reads
c) This is not sure, because I can't track back what I think I saw: the opposite to a) - scores from second command were worse than those from first.
Could you explain me why?