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Old 06-28-2012, 01:36 PM   #1
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Location: Austria

Join Date: Jun 2012
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Default Problems using GATK for variant calling


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?
pooja_singh is offline   Reply With Quote
Old 07-07-2012, 11:23 AM   #2
Location: New York, NY

Join Date: Oct 2011
Posts: 41

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.
jflowers is offline   Reply With Quote

gatk, rnaseq, tophat, transcript mapping

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