Weird Duplicated Lines With Gatk

Question

[Gabriel R.]

Hi all,

I came across weird lines produced by GATK and I was wondering if anyone ever came across a similar problem.

I have two lines for the same position (but no indel):

chr19    9413330    .    G    T    529.48    .GT:DP:GQ:PL  0/1:111:99:559,0,2802
chr19    9413330    .    G    .    16.10    LowQual    GT:DP:GQ:PL  0/0:106:0.02:23,0,2904

I understand having multiple lines for indels but what do these lines even mean ? I mean the sample is probably heterozygous at that position.

Thanks !

Answer 1

[Alex Paciorkowski]

It looks like your second read at chr19:9413330 is of low quality and there is no call. I would filter that read out of further analyses.

[Gabriel R.]

It's not a read, it's the output of the genotyper.

[Alex Paciorkowski]

Same idea. There's still no call at that site. I would still toss it.

And your sample is heterozygous at position. That's what 0/1 in your first "read" means.

[Gabriel R.]

I understand, the bottom line is that this line should not exist.