Heterozygous position called as Homozygous
Posted in Ask the team | Last updated on 2013-06-10 17:13:05


Comments (5)

Dear developers, I have looked into the forum for similar questions but I couldn't find any. I have several cases in which I get homozygous calls in positions with ~50% of reads calling the mutation (or less), please find here an example of a position validated by Sanger (as het) in which I have a high coverage (~400 reads in total) here is the results with UnifiedGenotyper:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  L1
chr4    998101  .       C       T       7296.77 .       AC=2;AF=1.00;AN=2;BaseQRankSum=16.344;DP=411;Dels=0.00;FS=0.000;HaplotypeScore=11.8258;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;MQRankSum=-1.436;QD=17.75;ReadPosRankSum=-0.062   GT:AD:DP:GQ:PL  1/1:203,208:411:99:7325,581,0

can you help me in this case? I am really puzzled.
I have run it with v2.2, 2.4 and 2.5 and I always had the same genotype call (the excerpt here is from the 2.5, I have downloaded it just to check it was not caused by a bug already fixed). It's not a downsampling issue since I have high coverage samples (HaloPlex) and used higher dcov than the default.


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