IMPUTE2: how to dynamically obtain chunks for each chromosome

I would like to run IMPUTE2 on some pre-phased data (made using SHAPEIT). The command I would like to use is like the example one given by IMPUTE2:

./impute2 \
-known_haps_g gwas_data_chr10_phased.haps \
-h pilot1.jun2010.b36.CEU.chr10.snpfilt.haps \
-l pilot1.jun2010.b36.CEU.chr10.snpfilt.legend \
-m genetic_map_chr10_combined_b36.txt \
-int 20000000 25000000 \
-Ne 15000 \
-buffer 250 \
-o gwas_data_chr10_imputed.20-25Mb.gen

I know it is best to split imputation in chromosome chunks (chunks of 5Mb here and set with the option -int). My question is how, given the file below which shows the chromosome and its size, is there a way I can dynamically obtain these chunks so I can write batch jobs?

1   249250621
2   243199373
3   198022430
4   191154276
5   180915260
6   171115067
etc

Many thanks.

impute2 chunks

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updated 6.1 years ago by jmukisa90 •

• written 6.1 years ago by m98

1 answer

Hi M93, It seems you have a similar problem like the one I had here:ERROR: You must specify a valid interval for imputation using the -int argument, -use_prephased_g: command not found, in IMPUTE2. The solution provided by Kevin will be helpful.

• 0 views • link

written 6.1 years ago by jmukisa90 •