bcftools convert imputed2 file error
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20 months ago
switch.reem ▴ 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?

bcftools covert impute2 • 489 views
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