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GenotyPE Concordance Error
I have generated multi-sample SNPs in VCF format following GATK best practice (gVCF generation + combinegVCF+GenotypegVCF+VQSR for SNPs) and trying to run GATK GenotypeConcordance between Genotype (muti-sample) in VCF and Haplotype Caller (multi-sample) VCF file as below:
java -jar /GATK/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T GenotypeConcordance -R /genomes/hg19/hg19.fa -eval 2500Sample_new_filtered.vcf.gz --comp Genotype_SNPs.vcf.gz --moltenize -o output_GenotypeConcordance_filtered.grp
I have cleaned up GenotypeVCF using vcftools to remove monomorphic alle sites. The error occurs like the following. Genotype header shows teh vcf format as below:
The provided VCF file is malformed at approximately line number 205771: Insertions/Deletions are not supported when reading 3.x VCF's. Please convert your file to VCF4 using VCFTools, available at http://vcftools.sourceforge.net/index.html, for input source: 2500Sample_new_filtered.vcf.gz -comp Genotype_SNPs.vcf.gz
Could you please throw some light on this error? Thanks.