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Strange results generated from HaplotypeCaller when comparing "-minPruning 3" with "-minPruning 2"
Hi GATK developer,
I am working on a human WES project with an average sequencing depth 42X per individual. Recent version of GATK (v3.2-2) was used in my study. To investigate which "-minPruning" setting is better for my project, I ran HaplotypeCaller and tested the "-minPruning 3" and "-minPruning 2", so I generate two sets of gvcf files. I found some interesting cases when I compared these two sets of files.
For example in the same individual (we name this individual as A):
Locus "chr1 1654007" from the GVCF file for individual A (-minPruning 3) is listed as below:
chr1 1654007 . A . . END=1654007 GT:DP:GQ:MIN_DP:PL 0/0:64:0:64:0,0,1922
Locus "chr1 1654007" from the GVCF file for individual A (-minPruning 2) is listed as below:
chr1 1654007 rs199558549 A T, 155.90 . DB;DP=6;MLEAC=2,0;MLEAF=1.00,0.00;MQ=27.73;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,6,0:6:18:189,18,0,189,18,189:0,0,4,2
You can see it is quite different for the results in terms of the final genotyping call and the sequencing depth ("DP" tag) generated from "-minPruning 3" and "-minPruning 2" setting. I am wondering what exactly happens for this locus so I check this locus using IGV. I found at this locus, there are 6 reads supporting the ALT allele ("T") and 64 reads supporting the REF allele ("A"). So I believe the result from "-minPruning 3" should be correct.
Just wondering is it normal considering the different setting of "-minPruning 3" and "-minPruning 2"or is it just a bug? If it is just because of the different setting of "-minPruning 3" and "-minPruning 2", I would say the setting of "-minPruning" is critical for the final results so a guideline of how to set the "-minPruning" based on the sequencing depth will be important. How do you think?