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Old 08-01-2012, 11:24 PM   #1
Karen Chait Berman
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Location: Israel

Join Date: May 2012
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Default GATK alternate alleles

I am running variant calling with GATK and I am getting variants with only one alternate allele. Running the same bam file with samtools, I got variants with more then one alternate allele. Is there a missing parameter in my command or is GATK outputing only the most probable allele?

java -Xmx2g -jar /illumina/bin/GenomeAnalysisTK-1.6-13-g91f02df/GenomeAnalysisTK.jar -I sorted_2012.unique.bam -R genomes/Tomato_2.40/S_lycopersicum_chromosomes.2.40.fa -T UnifiedGenotyper -o 2012.vcf > gatkGenotyper.out

Thanks,
Karen

Last edited by Karen Chait Berman; 08-01-2012 at 11:33 PM.
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Old 08-02-2012, 06:23 AM   #2
sdarko
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Default

The pre-release version of novoutil is able to do what you need. I had the same problem.

http://www.novocraft.com/wiki/tiki-v...=691#threadId1

Sam
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