Legend and hap files for imputation with 38 build

Question

[anahit]

Hi, I want to impute my data genotyped with 38 build. Where can I find legend and hap files for 38 build?

I am trying to use vcf2impute_legend_haps script provided by IMPUTE2, but it does not give me any results with vcf files downloaded from here http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/

Thank you!

[4galaxy77]

Really you should be using the most recent version, impute5, as imputed2 is very old now. If you use impute5, it will be much faster and you can directly use vcf files rather than having to convert them into some exotic format.

[anahit]

Thank you! My goal is to merge two reference panels and then conduct the imputation. I checked IMPUTE5, but not sure that there is an option for that..

[4galaxy77]

There is an option to use a reference panel? Why do you think there isn't?

[anahit]

I could not find -merge_ref_panels flag as in IMPUTE2 manual here https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#-merge_ref_panels

[4galaxy77]

OK - you could merge them together using bcftools --merge if they are in vcf format and then use the output in IMPUTE5 or another more recent software.

[anahit]

Thank you very much for your help! Would you recommend phasing with SHAPEIT2? As I understand, there is a possibility to phase with and without using the reference panel, though with the last option I need again legend/hap formats.

[4galaxy77]

If you want to pre-phase then use shapeit4 as it is the most recent version and will save you a lot of time since i) you can use vcf/bcf and directly and then use them with IMPUTE5 and ii) it's a lot faster. What size is the dataset you are phasing? If it's less than say, 2000 individuals then I would probably recommend using a reference panel, definitely if it's less than 100 samples. both shapeit4 and impute5 allow you to use reference panels.

[anahit]

My samples size is 35 samples. Thank you very much!

[anahit]

Hi, Sorry do you know any method (software, script), which I can use to compare the imputed data in vcf format? I would like to get Rsqv for position? Thank you very much!