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I've been using MiSeq Reporter ever since I started using the MiSeq and it's been working pretty well for just about everything I threw at it (custom amplicon and Nextera assays). However lately I noticed that it failed to call some major mutations such as KRAS G12D at 54% and single nucleotide indels (from TruSight Myeloid runs). I only caught these when browsing the .bam files in IGV and comparing with a separate analysis on BaseSpace. I've been using the Somatic Variant Caller with default filter settings in MSR and BaseSpace for all of these cases. Since MSR uses an older version of GATK, BaseSpace has been buggy lately, and BaseSpace Onsite does not support custom amplicon assays, there should be 3rd party solutions for this.
From my understanding variant callers such as GATK are primarily used for WGS and WES however the last time I tried using the Haplotype Caller -nct 8 for aligning TruSight Myeloid samples, the program would crash 10 minutes later saying it ran out of memory (I have 16 GB of RAM on an 8-core Xeon E5-2650). The samples have a mean coverage of 5000x and cover roughly 50 genes. Aligning reads to the manifest file Illumina supplied instead of the whole genome should save a lot of time as well.
So how should I go about doing this? Does GATK have a more suitable caller or should I go with something entirely different?
From my understanding variant callers such as GATK are primarily used for WGS and WES however the last time I tried using the Haplotype Caller -nct 8 for aligning TruSight Myeloid samples, the program would crash 10 minutes later saying it ran out of memory (I have 16 GB of RAM on an 8-core Xeon E5-2650). The samples have a mean coverage of 5000x and cover roughly 50 genes. Aligning reads to the manifest file Illumina supplied instead of the whole genome should save a lot of time as well.
So how should I go about doing this? Does GATK have a more suitable caller or should I go with something entirely different?