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Genotype caller discrepancies
I have found some discrepancies in the genotype call via GATK and the read fields and would like some help to explain what these mean. This analysis was done using GATK v1.2-12-g15a410b.
a) I have found a genotype call which is not 0/0, 0/1 or 1/1 - what does this mean?
2/2:17,14,1:140:36.84:2375,2267,3131,196,37,0 (Note there is no other variant called at this position)
b) I found a variant with an extra number in the alt read field, and wonder which number is the true alt read?
c) GATK has called a heterozygous call at this position in my data, but when i viewed the bam file on IGV, I could not find the same variant call.
d) GATK has appropriately called a het call for this variant, but the alt reads are listed as 0.