New features in IMPUTE v2.2

• IMPUTE2 can now handle datasets from human chromosome X. You can read about the relevant command-line options here, learn the file formatting conventions here, and see an example application here.


• The software can now handle insertion/deletion and structural variants, like the kind found in the 1,000 Genomes Phase 1 integrated variant dataset. This means that the program will accept arbitrary alleles (e.g., 'ACGGAAT' or 'DEL') and multiple reference variants (e.g., a SNP at the same position as an INDEL) at the same site.


• To reduce the computing cost of imputation with sequence-based reference panels, IMPUTE2 now allows you to flexibly remove variants from the reference panel at runtime. This filtering step is activated by the -filt_rules_l option. For an example of how to apply this option, along with some usage guidelines, see here.


• We have streamlined IMPUTE2's "pre-phasing" functionality by introducing the -prephase_g and -use_prephased_g flags. For an example of how these new options work, see here.


• The -fix_strand_g and -fix_strand_g_ref flags have been replaced by flags named -align_by_maf_g and -align_by_maf_g_ref.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.


• 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.