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How do I use CombineVariants to combine snps and Indels ?
When I use the following command to combine snp and INDEL calls from the same sample, they appear as two samples in the output-vcf. Hence, I also get two lanes with genotype-info, one for the Indels, and one for the snps. Is there a way to combine them so that the output vcf have only one lane of genotype-info?
java -Xmx8g -jar ' . $GATKdir . 'GenomeAnalysisTK.jar \\ -R ' . $hg19ref . '.fasta \\ -T CombineVariants \\ --variant snp.vqsr.filter.vcf \\ --variant indel.filter.vcf \\ -o ' . $fname . 'CombinedVariants.filter.vcf \\ -genotypeMergeOptions UNIQUIFY \\ 2>errCombineVar > CombineVarInfo.txt