Problems using GATK for variant calling

[pooja_singh]

Hi,

I am busy working with Eucalyptus transcriptome data generated using the Illumina platform. I mapped the paired end reads using TopHat and cufflinks. Then I defined read groups using Picard tools and sorted and indexed the BAM files using SAM tools. Now I am trying to use GATK to call variants using the BAM files as input. However, i can't carry out the step where you 'realign around known indels' since there aren't any for this species. So when I skip this step and go straight to calling SNP and indels i get an unknown error:

old_5354, scaffold_5355, scaffold_5356, scaffold_5357, scaffold_5358, scaffold_5359, scaffold_5360, scaffold_5361, scaffold_5362, scaffold_5363, scaffold_5364, scaffold_5365, scaffold_5366, scaffold_5367, scaffold_5368, scaffold_5369, scaffold_5370, scaffold_5371, scaffold_5372, scaffold_5373, scaffold_5374, scaffold_5375, scaffold_5376, scaffold_5377, scaffold_5378, scaffold_5379]
##### ERROR --------------------------------------------------------------------------

I really am not sure how to fix this since this is the first time that I am working with RNAseq data. Does anyone have any solutions?

[jflowers]

You don't need to have known indels. The --known argument in the RealignerTargetCreator and IndelRealigner is optional. You should however run both the target creator and realigner for best alignment results.