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Old 11-20-2012, 11:14 PM   #1
bioinf newbie
Location: India

Join Date: Feb 2012
Posts: 13
Default GATK LiftOverVariants input vcf

I am trying to convert a vcf file of b36 build to hg19.
First few line of my vcf file:

##INFO=<ID=Database,Number=1,Type=String,Description="Database identifier">
##INFO=<ID=Dbxref,Number=.,Type=String,Description="Database reference">
##INFO=<ID=dbID,Number=1,Type=String,Description="Database identifier">
##INFO=<ID=ID,Number=.,Type=String,Description="Chromosome or contig">
##INFO=<ID=Alias,Number=.,Type=String,Description="Mostly novel variant">
##INFO=<ID=Variant_seq,Number=.,Type=String,Description="Alternate Allele">
##INFO=<ID=Genotype,Number=.,Type=String,Description="Homozyguous or Heterozyguous">
##INFO=<ID=Variant_reads,Number=.,Type=Integer,Description="Number of reads where variant present">
##INFO=<ID=Total_reads,Number=.,Type=Integer,Description="Total number of reads">
##INFO=<ID=Reference_seq,Number=1,Type=String,Description="Ancestral allele">
chr1 4793 . A G 25 . ID=chr1:SoapSNP:SNV:4793;Alias=YHSNP0128643;Variant_seq=A,G;Reference_seq=A;Variant_reads=48,26;Total_reads=74;Genotype=heterozygous
chr1 6434 . G A 48 . ID=chr1:SoapSNP:SNV:6434;Alias=YHSNP0128644;Variant_seq=A,G;Reference_seq=G;Variant_reads=10,11;Total_reads=21;Genotype=heterozygous
chr1 93896 rs4287120 T C 51 . ID=chr1:SoapSNP:SNV:93896;Dbxref=dbSNP:rs4287120;Variant_seq=C,T;Reference_seq=T;Variant_reads=5,4;Total_reads=9;Genotype=heterozygous
chr1 225707 rs6603780 C G 43 . ID=chr1:SoapSNP:SNV:225707;Dbxref=dbSNP:rs6603780;Variant_seq=C,G;Reference_seq=C;Variant_reads=23,12;Total_reads=35;Genotype=heterozygous
chr1 225839 rs6422503 C A 31 . ID=chr1:SoapSNP:SNV:225839;Dbxref=dbSNP:rs6422503;Variant_seq=A,C;Reference_seq=C;Variant_reads=13,5;Total_reads=18;Genotype=heterozygous
chr1 526849 . G T 76 . ID=chr1:SoapSNP:SNV:526849;Alias=YHSNP0128645;Variant_seq=G,T;Reference_seq=G;Variant_reads=14,12;Total_reads=26;Genotype=heterozygous
chr1 554731 rs1832728 T C 30 . ID=chr1:SoapSNP:SNV:554731;Dbxref=dbSNP:rs1832728;Variant_seq=C,T;Reference_seq=T;Variant_reads=37,12;Total_reads=49;Genotype=heterozygous
chr1 555353 rs7349153 T C 28 . ID=chr1:SoapSNP:SNV:555353;Dbxref=dbSNP:rs7349153;Variant_seq=C,T;Reference_seq=T;Variant_reads=37,9;Total_reads=46;Genotype=heterozygous
chr1 555371 rs9283150 G A 22 .

I have the vcf file validated using vcftools vcf-validator. But when I use the LiftOverVariants tool, it gives me the error:
The providedVCF file is malformed at approximately line number 13: Trying to create a VariantContext with a ID key. Please use provided constructor argument ID.

Please can someone tell me how to fix this?
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build conversion, gatk, input vcf for gatk, liftovervariants

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