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UnifiedGenotyper: Multiple variants with the same coordinate?

antoinetonioantoinetonio Cambridge, UKMember

Dear GATK,

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,


Best Answer


  • antoinetonioantoinetonio Cambridge, UKMember

    Hi Sheila,

    Thanks a lot for your quick reply. A printscreen (from 'LookSeq') describing the issue is attached. The latest version of GATK did not fix the issue using UnifiedGenotyper. However, the good news is that the HaplotypeCaller did output the correct variant:
    Pf3D7_14 2261798 . T TTA,TTATATATA 17009.39 1:0,37,0:37:99:1202,0,1589

    (I did not know that HaplotypeCaller was now available for haploid genomes, that's great)

    Thanks again for this forum, it is very helpful!


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