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Old 07-08-2020, 04:12 AM   #1
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Location: Davis, CA

Join Date: Feb 2010
Posts: 10
Default Genotype call incorrect in freebayes output?

So I ran freebayes 1.3.1 with all the default parameters on dog dna samples. I am getting this result for one of the samples (although it seems to be occurring in other samples too):

37 20134611 GCCGGGGTGCCGGGGGCC GCCGGGGCC,GCGGGGGTGCCGGGGGCG,GCGGGGGCC,GCGGGGGTGCGGGGGGCG,GCGGGGGCG,GCCGGGGTGC GT:DP:AD:RO:QR:AO:QA:GL 3/3:24:0,22,0,0,0,0,0:0:0:22,0,0,0,0,0:418,0,0,0,0,0:-50.6989,-42.8808,-10.0438,-81.5228,-45.9661,-5.53744,-73.8782,-38.3406,-12.4611,0,-81.5228,-45.9661,-12.4611,-12.4611,-5.53744,-81.5228,-45.9661,-12.4611,-12.4611,-12.4611,-5.53744,-73.8782,-38.3406,-76.9605,-69.3158,-76.9605,-76.9605,-47.6417
I'm only showing the relevant columns. So the genotype call is 3/3, which is NOT correct from looking at the alignment there:

This implies that most of the reads should go to the 1/1 genotype call. And, the AD field looks like this:


There are 22 reads that contribute to the 1st alt allele and none to the others. So shouldn't the call be 1/1?

Last edited by najoshi; 07-08-2020 at 04:15 AM.
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Old 11-28-2020, 06:04 AM   #2
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Location: Ukraine

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I cant understand the difference between genotype and phenotype in this case. Found only this review

Last edited by kimaline; 11-29-2020 at 09:06 AM.
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freebayes, genotype, vcf

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