Error in performing imputation on chromosome X by using IMPUTE2 based on prephase results using SHAPEIT

Question

[guiming]

Dear all, I used SHAPEIT to prophase the data of plink format (with bed, bim, and fam), and then use IMPUTE2 to impute genotypes. I wrote code following the IMPUTE2 instruction, but IMPUTE2 does not generate any impute results. It shows error as below:

“  ERROR: When performing imputation on chromosome X, you must provide a sample file for each -g, -g_ref, and/or -known_haps_g input file.”

Did you have this problem before. I put my code for running SHAPEIT and IMPUTE2 below. IF you have experience of imputing Chromosome X, can you take a quick look and give some comments and suggestions? Thank you.

Code running SHAPEIT:

cd /group/huo-lab/TCGA/SNP6_level2/Gao/Shapeit/tcga_female_chr_bed

shapeit --input-bed tcga.female.chr23.bed  tcga.female.chr23.bim  tcga.female.chr23.fam  --input-map /group/huo-lab/TCGA/SNP6_level2/Gao/1000GP_Phase3_chrX/genetic_map_chrX_nonPAR_combined_b37.txt --output-max ../tcga_female_pre_phased/tcga.female.chr23_nonPAR.phased.haps ../tcga_female_pre_phased/tcga.female.chr23_nonPAR.phased.sample --thread 4 --chrX

Code running IMPUTE2

cd /group/huo-lab/TCGA/SNP6_level2/Gao/1000GP_Phase3_chrX

impute2 -use_prephased_g -chrX -m ./genetic_map_chrX_nonPAR_combined_b37.txt -h ./1000GP_Phase3_chrX_NONPAR.hap.gz -l ./1000GP_Phase3_chrX_NONPAR.legend.gz -known_haps_g ../Shapeit/tcga_female_pre_phased/tcga.female.chr23_nonPAR.phased.haps -int 2699520 7779363 -allow_large_regions -Ne 20000 -o ../imputed_data_chrX/tcga.chr23_nonPar.seg1.phased.impute2 -phase

Best wishes,

Guimin

[guiming]

add a sample file indicating male and female -sample_g ./Example/chrX/example.chrX.study.sample \

[814548364]

hello， I want to phasing whole Chromosome X，including PAR and non-PAR, I see you code, you only use non-PAR data and add argument --chrX, could you tell me how you deal with PAR region? just add --chrX? Thank you very much!