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HaplotypeCaller bias AGAINST heterozygous calls
I am having an issue with haplotypecaller omitting true heterozygotes. Attached is an IGV image of the VCF (top track), de novo reassembled BAM file (middle) and input BAM file (bottom). This appears to be happening all over. I was wondering what I can do to address this issue.
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ref.fasta -I sample.realigned.marked.sorted.bqsr.unique.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o sample.hapcal.raw.vcf -nct 12
p.s. I get the same results when running without multiple threads and when outputting the rearranged BAM file used for variant calling.