If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.