works on interactive node:
impute4.r265.1




IMPUTE4 
=====

Basic usage is 

./impute4.r260.2 \
-h example/1000GP_Phase3_chr20.hap.gz \
-l example/1000GP_Phase3_chr20.legend \
-m example/genetic_map_chr20_combined_b37.txt \
-g example/test.haps.gz \
-int 2000000 3000000 \
-buffer 500 \
-no_maf_align \
-Ne 20000 \
-snp_blocks \
-o_gz \
-o example/output

Explanation of options

-h <file> : reference panel haplotype file. Same input format as used by IMPUTE2
-l <file> : reference panel legend file. Same input format as used by IMPUTE2
-g <file> : phased samples to be imputed. Same input format as used by IMPUTE2
-m <file> : genetic map file. Same input format as used by IMPUTE2
-int <s> <e> : interval for imputation [s,e]
-buffer <kb> : buffer region each side of interval used in computation to avoid edge effects
-no_maf_align : flag that says don't do any alignment of alleles based on allele frequency 
-Ne 20000 : effective population size. Internal parameter. Safe to leave at 20000
-snp_blocks : internal flag that controls model used. Always use this.
-o_gz : gzip output files
-o <file> : specifies output file prefix
