[Question] information in the filter column of vcfs

[hangsuUNC]

[Question] information in the filter column of vcfs

[hangsuUNC]

Thanks so much!

[holtjma]

Hi Hang,

HiPhase does not look at the FILTER column currently, but it does filter on the GQ field if available; so in this case, it should read in "PASS", ".", or really anything as long as the VCF parser can parse it. If the GQ field does not work for what you want to remove, then I would recommend pre-filtering the variants in your VCF prior to calling HiPhase.

For reference, here's the function that checks if a variant is phase able or not, which is currently checking zygosity, GQ, and variant type:

HiPhase/src/block_gen.rs

Line 115 in 99b92ac

pub fn is_phasable_variant(record: &bcf::Record, sample_index: usize, min_quality: i32, is_hom_allowed: bool) -> Result<bool, Box<dyn std::error::Error>> {

Matt