automatic detection of false-positive large indels checking their GQ scores

Question

[bio.pelayo]

Hi, all.

I have a multisample vcf. Mi goal is to automate the detection of large indels that are possibly FP after the calling variant step. How could I parse the lenght of REF or ALT fileds to detect indels with more than 100 bases in lenght?

I share here an example

Any suggestion will be appreciated.

[Pierre Lindenbaum]

do you have the tags END or SVLEN in the INFO field ?

[bio.pelayo]

Hi, Pierre. No, I do not. INFO field is empty!