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HaplotypeCaller calling error

zhkzhouzhkzhou ChinaMember

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 \
-variant_index_type LINEAR \
-variant_index_parameter 128000

GATK.jpg 162.8K

Best Answer


  • zhkzhouzhkzhou ChinaMember

    Dear Geraldine,
    I couldn't found a resonable reason in "Common Problem" for why HaplotypeCaller missing some very obvious variation. Please check the attached picture, this is IGV debug process, but HC still missing at 146bp.
    Many thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If you mean the A allele at the site on the right, that looks more like an artifact to me... What does the GVCF record look like if you run on this site in -ERC BP_RESOLUTION?

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