I have generated 1 million 600bp single ended reads using Wgsim read simulator from chr21 of hg19. All the bases have 40 base quality. The reads are aligned with BWA-MEM and then sorted and deduplicated with Picard tools. No base recalibration is done. The haplotype caller of GATK 3.6 is finding 0 active regions and hence no variant is being called. I also tried with increased mutation rate but of no use. I found some other suggestions from past posts like using -forceActive and -disableOptimizations., but they are having no effect. Are Wgsim simulated reads not suitable for variant calling or there is something else?
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