genotype imputation errors
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2.3 years ago

I have used shapeit4 to phase my genotype data, and perform the genotype imputation on the phased .vcf.gz file by Impute4 software. Impute4 produce an .gen file as result. When I covert .gen to plink .bed file, I get following message

Error: Invalid chromosome code '##FILTER=<ID=PASS,Description="All' on line 1 of .gen file.
plink2 --gen test.gen --sample gen.sample --make-bed --out test

So, if there are some wrongs, when I do phasing and imputation?

phasing:

shapeit4 --input chr1.vcf.gz --map genetic_map_chr1_combined_b37.txt --region 1 --output chr1.phased.vcf.gz

imputation:

impute4.1.2_r300.2 
-h 1000GP_Phase3_chr1.hap.gz
-l 1000GP_Phase3_chr1.legend.gz
-m genetic_map_chr1_combined_b37.txt
-g chr1.phased.vcf.gz
-no_maf_align
-int 0 1000000
-buffer 2500
-o chr1
genome SNP software error • 646 views
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