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Dramatic decrease in the number of variants discovered after applying --ploidy

Hi! I did two haplotypecaller GVCF runs on DNA-Seq data, one with default ploidy 2 and one with ploidy 28 (my library is a pool of 14 diploid animal samples). I noticed there is a drastic decrease in the output raw.g.vcf when using ploidy 28. And when I did GenotypeGVCFs on two pooled samples, I didn't get any variants (comparing with 8 million variants when ploidy was 2). Both runs were successful, except there were some warns. When I used ploidy 28, I got a lot of warns like this:

WARN 01:07:07,013 HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 28 and original allele count is 6, whereas after trimming the allele count becomes 3. Alleles kept are:[G*, GA, GAA]

and 4 warns like this:

WARN 01:00:38,381 AFCalculator - Maximum allowed number of PLs (100) exceeded for sample 2 at 1:12116-12116 with 435 possible genotypes. No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) unless the --max_num_PL_values argument is increased accordingly. Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.

and only 1 warn like this:

WARN 16:46:45,794 AFCalculator - Maximum allowed number of PLs (100) was exceeded 5948937 time(s); the largest number of PLs found was 4495. No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) unless the --max_num_PL_values argument is increased accordingly.

Wonder if you know why this happened. Thank you for the help in advance.

Answers

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