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# Homozygous VS Heterozygous

Member Posts: 101

Hi,

I have two SNP calls as shown below:

The first SNP is categorized as 1/1 and the second SNP as 0/1. For both the SNP's the variant allele ratio are 30/32=0.9375 and 30/33=0.909 which are approximately equal and above 0.9. On what criteria one SNP is determined as 0/1 and the other as 1/1?

As per my knowledge both the SNPs should be 1/1. Could anyone comment the reason for this discrepancy?

Tagged:

If not and you still think there is a problem, could you please post what version of GATK you are using and the command line?

Geraldine Van der Auwera, PhD

• Member Posts: 101

Hi,

The second point seems to be applicable i.e. depth reported in the VCF is the unfiltered depth. But, here i have considered the filtered depth and im still unclear about the call.

I am using GATK version 2.4-9 and the command line is:

java -jar GenomeAnalysisTK.jar -glm SNP -R ref.fasta -T UnifiedGenotyper -I in.bam -o out.vcf.

Hmm. Could you run again on that interval using the latest version (2.6)? It would also help to see a screenshot of the pileup in IGV if possible.

Geraldine Van der Auwera, PhD

• Member Posts: 101

I have re-run it using GATK latest version and it called botht he SNPs as 1/1 and it looks fine. But what has been changed from the previous version to have a different call? Based on what criteria it calls as 1/1 or 0/1?