By viewing the alignment BAM file in IGV, we can observe a significant SNP at a position. All reads that mapped to that regions shows this single mutation.
However, with GATK's UnifiedGenotyper, this SNP has a very low QUAL value (QUAL=7).
Not sure what caused this confusion, so at now I am trying to use two mapping applications novoalign and BWA as aligner, and two genotyper application UnifiedGenotyper and samtool/mpileup to call variances.
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