Quantcast
Channel: haplotypecaller — GATK-Forum
Viewing all articles
Browse latest Browse all 1335

HaplotypeCaller not generating DP field

$
0
0

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?

Thanks


Viewing all articles
Browse latest Browse all 1335

Trending Articles