Hi there,

Could anyone explain me a little bit these two lines of my GVCF file?

Why I'm getting "NON REF" alternative allele? And why for the second line I only see END information and not the rest?

```
GL000192.1    546636    .    G    A,<NON_REF>    49.77    .    BaseQRankSum=1.026;ClippingRankSum=1.026;DP=4;MLEAC=1,0;MLEAF=0.500,0.00;MQ=49.02;MQ0=0;MQRankSum=-1.026;ReadPosRankSum=0.000    GT:AD:DP:GQ:PGT:PID:PL:SB    0/1:2,2,0:4:78:0|1:546636_G_A:78,0,87,84,93,177:1,1,1,1
GL000192.1    546637    .    G    <NON_REF>    .    .    END=546645    GT:DP:GQ:MIN_DP:PL    0/0:4:11:4:0,12,99
```

I know that `NON_REF` represents any possible alternative allele at this location, but if my genotype is 0/0 (homozygous for reference)... this line makes no sense for me.

Thanks in advance.
<p>OK, I found the solution in GATK manual (<a href="https://www.broadinstitute.org/gatk/guide/article?id=4017">https://www.broadinstitute.org/gatk/guide/article?id=4017</a>). I&#39;ll answer my own question just in case that someone else have the same issue.</p>

<p><em>&quot;The first thing you&#39;ll notice, hopefully, is the <code>&lt;NON_REF&gt;</code> symbolic allele listed in every record&#39;s <code>ALT</code> field. This provides us with a way to represent the possibility of having a non-reference allele at this site, and to indicate our confidence either way.</em></p>

<p><em>The second thing to look for is the <code>END</code> tag in the <code>INFO</code> field of non-variant block records. This tells you at what position the block ends.&quot;</em></p>
