Haplotype Caller calls variants where there are no reads?
Basically, i'm seeing variants called where I have no reads. Not sure why, but maybe the developers might know why?
All the data needed to replicate this can be found at http://ac.gt/haplotypecaller.tar.gz
I saw this when I created the g.vcf on the full BAM file with the full genome.fa, but I also tried re-making the g.vcf with just the reads around the variant, and a genome.fa of just chromosome 1. It gave the same result so the above link just that data from which you can re-run:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ./genome.fa -I ./input.bam --emitRefConfidence GVCF -o ./output.g.vcf