GATK alternate alleles

[Karen Chait Berman]

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

[sdarko]

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

http://www.novocraft.com/wiki/tiki-view_forum_thread.php?forumId=1&comments_parentId=691#threadId1

Sam