Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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