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  • Using GATK to call SNPs in RNA-seq data

    has anyone ever used SNP calling from RNA-seq data?
    I am currently trying to do this but GATK is calling the reference as the variant??? I have checked my reference file and it's perfectly correct.

    I don't know if this a result from me using RNA-seq or just my command.

    I am using an older version of gatk because it doesn't require the extensive file modifications that is required of the newer versions.

    My command is below:

    GenomeAnalysisTK.jar
    -T UnifiedGenotyper
    -l INFO
    -I file.bam
    -R Homo_sapiens_assembly18.fasta
    -U ALLOW_UNINDEXED_BAM
    --assume_single_sample_reads sample_name
    --platform SOLEXA
    -dcov 300
    -varout file.vcf
    -nt 1
    -bad_mates

    any advice?

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