Imputation with Beagle 5.2 for whole exome data at once

Question

[L_to_the_m]

Hi, I have a vcf file of whole exome SNP data from multiple humans. No I want to impute the low call rates with Beagle v.5.2 and would therefore use the reference panel which is given on the website of Beagle (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/). Is there a way to infer all low call rate SNPs of the whole exome at once? And not imputing it per chromosome?

[4galaxy77]

It doesn't really make sense to do the whole genome at once because each chromosome is imputed seperately (because there is no linkage between different chromosomes). It is also much faster to run it in parallel (i.e. running each chromosome separately), if you have the computational resources. Otherwise, just write a simple for loop in bash for i in {1..22}; do impute; done. Also you will get much better results using the new updated 30x reference panel https://www.internationalgenome.org/data-portal/data-collection/30x-grch38