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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.