ploidy level in HaplotypeCaller and GenotypeGVCFs
I am trying to make SNP calling of chloroplast DNA reads from 85 samples, using GATK v4.0.
First, I used HaplotypeCaller to produce individual GVCF with the default ploidy setting. Making joint call using GenotypeGVCFs, and it only took a few minutes. But then I think the sample ploidy should set as 1, since I am working with chloroplast data.
I did not change any settings but only added “-ploidy 1” when running HaplotypeCaller and it worked. However, when running “gatk GenotypeGVCFs” with default settings, the program hanged at “WARN InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples” for hours and hours. Then I tried “-ploidy 85” when running GenotypeGVCFs but got the same problem.
I wonder what is wrong with the ploidy setting.
Also, I found HaplotypeCaller with “-ploidy 1” detected much fewer SNPs, comparing to the running with the default setting. I assume this is reasonable, right?
Looking forward to reply! Thanks a lot in advance!