Hello GATK team,
I have called variants with HaplotyeCaller in the whole exome data of 6 people (4 affected males and 2 unaffected). All 4 male patients are heterozygous for three variants in a gene located on the X chormosome. One of the unaffected who is the father of one patient is homozygous for reference allele while the other unaffected who is the mother of two of patients is heterozygous for the same variants (which makes sense)
I have checked the bamout from HC and it confirms what I see in the VCF. You can see the command I used below.
why does the caller decided to call the sons of the unaffected mother heterozygous? Can't HaplotypeCaller distinguish between male and female samples? Moreover, the number of reads showing the ALT allele is more than the REF in all three variant locations so I am confused about what the actual status of patients is.
GATK \
-T HaplotypeCaller \
-R ucsc.hg19.fasta \
-I recalibrated_reads_final.bam \
--genotyping_mode DISCOVERY \
-bamout bamout.bam \
--dbsnp dbsnp_138.hg19.vcf \
-A Coverage -A TandemRepeatAnnotator -A QualByDepth -A VariantType \
-o raw.vcf