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3.6 years ago
switch.reem
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40
Dear all,
I used Impute2 for genome imputation. the generated gen file is available and I am trying to generate a vcf version. for that I am using bcftools convert command.
when I run the convert -G imputation_with_crossvalidation_masked_1000_gen I get the below error message:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
##contig=<ID=chr16,length=2147483647>
##bcftools_convertVersion=1.9+htslib-1.9
##bcftools_convertCommand=convert -G imputation_with_crossvalidation_masked_1000_gen; Date=Mon Sep 7 11:07:19 2020
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 120136 120227 120206 13098 12560 120067 12718 13541 10737 120535 120324 13526 120089 10925 12850 12657 12960 10698 10411 12553 10926 12750 120200 120118 10556 10930 10205 13177 120013 12754
chr16 20400139 . C T . . . GT:GP 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:0.33,0.33,0.33 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:0.33,0.33,0.33 0/0:1,0,0 0/0:1,0,0 0/0:1,0,0 0/0:0.33,0.33,0.33
Could not determine sequence name or multiple sequences present: 16
here is a sample of my gen file
chr16:20400139_C_T chr16:20400139_C_T 20400139 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330$
chr16:20400174_C_T chr16:20400174_C_T 20400174 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0$
chr16:20400175_G_A chr16:20400175_G_A 20400175 G A 0 1 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330 1 0 0 1 0 0 1 0 0 0 1 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.330 0.330 0.330 1 0 0 0 1 0 0 1 0 1 0 0 1 0 0 1 0 0 0 1 0 0.330 0.330 0.330$
chr16:20400207_C_T chr16:20400207_C_T 20400207 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.962 0.038 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.863 0.137 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0$
chr16:20400229_C_T chr16:20400229_C_T 20400229 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.900 0.100 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0$
chr16:20400234_C_CA chr16:20400234_C_CA 20400234 CA C 0 1 0 0 0 1 0 0 1 0 0 1 0 0 1 0 1 0 0 0 1 0.330 0.330 0.330 0 0 1 0 1 0 0 0 1 0.330 0.330 0.330 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0.330 0.330 0.330 0 0 1 0 1 0 0 1 0 0 1 0 0 0 1 0 0 1 0 1 0 0.330 0.330 0.330$
chr16:20400260_G_T chr16:20400260_G_T 20400260 G T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.998 0.002 0 1 0 0 0.998 0.002 0 1 0 0 0.995 0.005 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0$
any idea what does that mean?
