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Increase sensitivity of HaplotypeCaller

GATK v4.1.3.0


I need to increase the sensitivity of HaplotypeCaller and test it because I have an heterozygous variant no called. We confirmed it by Sanger sequencing and I can see it in the bamout file.

Here is my HaplotypeCaller code (for CNN pipeline)

${GATK4} HaplotypeCaller \
-R ${hg38} \
-I ${BAM} \
-O ${VCF} \
-bamout ${bamout} \
-L ${inteval} \
-ip ${ipHC} \
--max-mnp-distance "1" \
--dont-trim-active-regions \
-stand-call-conf "0" \
-A Coverage \
-A ChromosomeCounts \
-A BaseQuality \
-A FragmentLength \
-A MappingQuality \
-A ReadPosition

Do you have any link or recommendation about what I have to change or option to add and value to modify?

Manu thanks


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