Hi, I have been trying to get a dosage file from vcf, map and fam files. For that, I have written this bash script :
plink –fam plink.fam –map plink.map –dosage one.vcf –write-dosage
However, I got this error:
–dosage: Reading from one.vcf.
Error: Line 1 of one.vcf has fewer tokens than expected.
The problem is from vcf file but I am reviewing this vcf file and I am not able to find the error. The file looks like that:
fileformat=VCFv4.2
fileDate=20210920
filedate=20210914
source=”beagle.28Jun21.220.jar”
FILTER=All filters passed
INFO=<ID=AF,Number=A,Type=Float,Description=”Estimated ALT Allele Frequencies”>
INFO=<ID=DR2,Number=A,Type=Float,Description=”Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2P(RR)] and true REF dose”>
INFO=<ID=IMP,Number=0,Type=Flag,Description=”Imputed marker”>
FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”>
FORMAT=<ID=DS,Number=A,Type=Float,Description=”estimated ALT dose [P(RA) + 2P(AA)]”>
contig=<ID=1,assembly=”hg38″>
contig=<ID=2,assembly=”hg38″>
contig=<ID=3,assembly=”hg38″>
contig=<ID=4,assembly=”hg38″>
contig=<ID=5,assembly=”hg38″>
….
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MR001_MR001
1 792461 GSA-rs116587930 G A . PASS . GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 1|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0
Please, help!!
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