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With the vcf output from GATK, I used SelectVariants to select variants with the following conditions:
java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \ -T SelectVariants \ -R GATK_ref/hg19.fasta \ -nt 5 \ -V ../GATK/VQSR/parallel_batch/Indels/exome.indels.filtered.vcf \ --excludeNonVariants \ -o ../GATK/VQSR/parallel_batch/Indels/exome.indels.filtered.selected.vcf \ -selectType INDEL \ -select "DP > 30.0"
In the output file exome.indels.filtered.selected.vcf, however, I find some variants have DP < 30, for example:
The bold highlighted 3 is the DP, does this mean SelectVariants did not work on my vcf?