Gatk Somaticindeldetector Vcf Info Field Missing

Question

[Mdeng]

Hey everyone,

I am a bit confused. I called my INDELs pairwise using the SomaticIndelDetector. But in the resulting VCF the info field seems to be missing, is this normal? Or am I getting something wrong?

The output looks like this:

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    ffpe
chr1    14947    .    C    CA    .    .    .    GT:AD:DP:MM:MQS:NQSBQ:NQSMM:REnd:RStart:SC 0/1:2,2:6:2.0,1.5:255.0,199.75:24.421053,31.571428:0.10526316,0.08571429:15,1:34,1:2,0,4,0

Sry for the poor format, here is also a hastebin version.

Could it be, that for pairwise callings scores are not possible?

With best,

Mario

[Arun]

You should search in GATK get satisfaction forum: getsatisfaction.com/gsa Else post a question there. You've more chances of getting a response there.