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I am using GATK 2.5, and am calling HaplotypeCaller as
java -Xmx4g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T HaplotypeCaller -I sample.bam -o hap.vcf -L subset.bed -dt NONE -D dbsnp_137.b37_addChr.vcf -filterNoBases -A Coverage -A DepthPerAlleleBySample
In the output vcf file, in the FORMAT field, I have GT:AD:GQ:PL. DP is lost. Even though it is specified in the header. UnifiedGenotyper is working fine, and producing DP information. Any ideas on what is wrong?