**Hi everyone**

I would like to take a second opinion regarding a variant with DP =17. The variant is in a very high GC content area so the low coverage is reasonable. 

I do hard filtering because I have few samples for VQSR, I thinks it is okay according to GATK hard filtering, the values are as follows:


       AC=1;AF=0.500;AN=2;BaseQRankSum=0.892;ClippingRankSum=0.000;DP=17;ExcessHet=3.0103;FS=10.843;
        MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.81;ReadPosRankSum=-1.534;
    SOR=2.795       GT:AD:DP:GQ:PL  0/1:14,3:17:76:76,0,506

I am worried because **AD is 14,3** which means only 3 reads only support the ALT? is it safe to accept it as  a het variant. The variant is very interesting based on our data, so I don't wanna discard without a strong reason. 

**Any comments, how do you think? with many many thanks**

I cannot provide a detailed answer given the information but a few comments. 

There are 2 most likely models:
1) The site is homozygous reference

Therefore, the 3 reads are potentially a) mismapped, b) weird duplicates or c) sequencing errors.

a) Did you use a mappability filter? i recommend Heng Li's method lh3lh3.users.sourceforge.net/snpable.shtml
b) Did you use rmdup?
c) if both a) and b) are satisfied, then they are sequencing errors, assuming a base quality of 38, the probability of 3 seq. errors occurring independently is:

(10^((-1*38)/10))^3 = 3.981072e-12

so one chance in 250 billion.

2) The site is heterozygous reference

It is possible that this is a genuine het site and you haven't sampled the other base, this can happen with probability:

dbinom(3,17,prob=0.5) =  0.005187988

so 1 chance in ~200 (assuming no mismappings or errors).

This is reflected in your PL field where the homo ref model has a score of 76, the het model a score of 0 (most likely) and 506 for the homo alt. While the hetero is more likely that the homo ref, it is not astronomically more likely. However, the homo alt is so unlikely that it can be safely discarded.

