The -fix_strand_g and -fix_strand_g_ref flags have been replaced by flags named -align_by_maf_g and -align_by_maf_g_ref. Whereas the old flags aligned variants across different panels by allele labels (which is natural) and MAFs (which can be dangerous for variants with frequencies near 50%), the new flags align variants using MAFs only; alignment by allele labels is now performed automatically.
The -pgs flag now works when imputing into pre-phased haplotypes, as long as you use it together with a new flag named -use_prephased_haps.
Imputation can be time-consuming with the latest 1,000 Genomes reference panels, even when imputing into pre-phased GWAS haplotypes. To reduce the computing cost of imputation, IMPUTE2 now allows you to flexibly remove underpowered variants from the reference panel at runtime. This filtering step is activated by the -l_filt flag, which uses a syntax like the following:
In this example, the strings 'afr.maf' and 'eur.maf' correspond to labeled columns in a legend file like the ones in this download package. The conditional statements implied by these strings are applied in 'or' fashion; i.e., this command-line statement tells IMPUTE2 to ignore any reference SNPs with MAF less than/equal to 5% in people of African ancestry OR MAF less than 0.1% in people of European ancestry.
IMPUTE2 now produces more concise screen output by default. If you want to see more detailed screen output, just supply the -verbose flag on the command line.