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  • 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, 11:33 PM.

  • #2
    The pre-release version of novoutil is able to do what you need. I had the same problem.



    Sam

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