Calling zero mapping quality variant

Question

[sonsunjirachote]

Hello

Is it possible to call variant with read that has zero mapping quality at the region?

I found that there is INDEL in my BAM file when I visualize in IGV but the variant is not in gVCF, I have checked the average MAPQ at that position is zero

I tried to adjust the parameters of haplotypecaller but still not working

java -Xmx32G -jar ~/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -R hg19.fa -I my.sorted.bam -O my.gvcf -ERC GVCF --dbsnp dbSNP154.hg19.vcf.gz --min-base-quality-score 5 -stand-call-conf 15 --max-alternate-alleles 3 --min-dangling-branch-length 2 --kmer-size 18 --kmer-size 22 --base-quality-score-threshold 6

Thanks in advance

JK

[lacb]

Have you used bwa to align? If this is the case, it could be that read maps to multiple locations : What Does The Zero Mapping Quality Mean For The Bwa Mapper?