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GATK_HaplotypeCaller: <NON_REF> .
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2.9 years ago
iraun ♦ 3.5k
Norway

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.

GATK • 3.3k views
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Indeed it is a very interesting question, my lady.

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2.9 years ago
iraun ♦ 3.5k
Norway

OK, I found the solution in GATK manual (https://www.broadinstitute.org/gatk/guide/article?id=4017). I'll answer my own question just in case that someone else have the same issue.

_" The first thing you'll notice, hopefully, is the <NON_REF> symbolic allele listed in every record's ALT 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._

The second thing to look for is theEND tag in the INFO field of non-variant block records. This tells you at what position the block ends."

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Thanks for following up!

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