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 to relax parameters in GenotypeGVCFs to get more variants?
I am using GenotypeGVCFs in following command,
java -Xmx2g -jar CancerAnalysisPackage-2015.1-3/GenomeAnalysisTK.jar -T GenotypeGVCFs -R Refgenome_ucsc/ucsc.hg19.fasta --variant chrn.g.vcf --out chrn
.rawVariants.vcf -L chrn.bed --interval_padding 100 --disable_auto_index_creation_and_locking_when_reading_rods -nt 4
no of variants in chrn.g.vcf = 12248378
no of variant in chrn.rawVariants.vcf = 85579
Is there any way to get more variants as i miss lot of vairants during this step? Please help me out as i am in great need.