Filter HOM_REF records without GQ information

[biozzq]

Instructions

Feature request

When filtering the variants, I found that genotypes without GQ information have been filtered. I wonder that if can add any parameter to change this default behavior. For example, if genotypes do not have GQ or any other tags, we can assume them to be PASS.

Tool(s) involved

Tool name(s), special parameters?
FilterVcf
java -Xmx20g -Djava.io.tmpdir=${tmp} -jar picard.jar FilterVcf --MIN_DP 3 --MIN_GQ 20 --INPUT ${chr}.raw.vcf.gz --OUTPUT ${chr}.flag.vcf.gz --CREATE_INDEX true

Description

Specify whether you want a modification of an existing behavior or addition of a new capability.
Provide examples, screenshots, where appropriate.
1 23454 rs1109686627 C . 132.87 PASS AN=32;DP=568 GT:AD:DP:FT 0/0:33:33:LowGQ 0/0:38:38:LowGQ 0/0:33:33:LowGQ 0/0:35:35:LowGQ 0/0:36:36:LowGQ 0/0:36:36:LowGQ 0/0:35:35:LowGQ 0/0:45:45:LowGQ 0/0:36:36:LowGQ 0/0:35:35:LowGQ 0/0:33:33:LowGQ 0/0:34:34:LowGQ 0/0:34:34:LowGQ 0/0:35:35:LowGQ 0/0:36:36:LowGQ 0/0:34:34:LowGQ

I want to keep these non-variant sites, thus I ask for your help here. Thank you in advance.

Best wishes,
Zheng zhuqing