How to set parameter in UnifiedGenotype mode like samtools mpileup
I want to filt out shared SNPs and Indels between two vcf files generate from samtools mpileup and GATK UnifiedGenotyper with SelectVariants.
With samtools, I can set the mapping quality, filter out the variants not within an interval and then generating a new vcf to know how many variants with such command
samtools mpileup -C50 -q25 -uf reference.fa input.bam | bcftools call -c | vcfutils.pl varFilter -d5 -D30 > output.vcf
However, from the manual of GATK 3 UnifiedGenotyper, I didn't find out what arguments I can set the interval I want.
What i only know is that UnifiedGenotyper take the coverage of the input beneath 250
Is there any tools of argument in GATK 3 to generate vcf and filt the coverage at the same time?
Thanks for help