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HaplotypeCaller calling error
I found many calling errors like this, all of the phred quality >30, but HaplotypeCaller miss them, report as Homozygote.
How to deal with it?
Here is the code. Many thanks.
java -Xmx200g -jar /home/share/bin/GenomeAnalysisTK-3.5.jar \
-R /home/share/index/Prunus_persica.fa \
-T HaplotypeCaller -nct 8 \
-I $d'.sorted.uniqe.rg.dedup.realn.bam' \
-o $d'.gvcf' \
--genotyping_mode DISCOVERY \
-stand_emit_conf 30 \
-stand_call_conf 30 \
-ERC GVCF \
-variant_index_type LINEAR \