UnifiedGenotyper: Multiple variants with the same coordinate?
I've got an issue using the UnifiedGenotyper, it does not output all possible variants sharing the same start coordinate.
My command line:
GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T UnifiedGenotyper -R ReferenceGenome.fasta -I list_of_Samples.list -ploidy 1 -glm BOTH --heterozygosity 0.001 --indel_heterozygosity 0.005 -gt_mode DISCOVERY -dcov 1000 -o output_raw_variants.vcf
Using "Batch 1" , about 50 Plasmodium falciparum samples, I identified the following insertion in Sample1, which I know is real :
chrom14 2261798 . T TTA 1576.91 1:2,42:59:99:1:1.00:1609,0
However when I run the same command line with Batch1 + Batch2, total of 100 samples, I get the following result for Sample1:
chrom14 2261798 . T TTATATA 23812.75 0:39,5:59:99:0:0.00:0,775
Some samples from Batch2 have a longer insertion starting at the same coordinate, and now the original insertion in Sample1 does not appear in the VCF anymore...
Why UnifiedGenotyper did not output multiple lines in this example? (for some other positions it did output multiple lines sharing the same coordinate)
I did not change the parameter --max_alternate_alleles 6.
Thanks a lot in advance for your help,