Add variants_filter_lcr, variants_filter_segdup and variants_snv_only options to annotate_sex to filter variants prior to variant only ploidy imputation

[jkgoodrich]

NOTE: This PR is stacked on the add_gaussian_karyotype PR #478

If helpful for testing:

import hail as hl
from gnomad_qc.v4.resources.basics import (
    calling_intervals,
    get_gnomad_v4_vds,
)
from bokeh.plotting import output_notebook, show

hl.init(default_reference='GRCh38')
output_notebook()

vds = get_gnomad_v4_vds(
    remove_hard_filtered_samples=False,
    remove_hard_filtered_samples_no_sex=True,
    test=True,
)
mt = hl.vds.to_merged_sparse_mt(vds)
calling_intervals=calling_intervals(interval_name='intersection', calling_interval_padding=50).ht()
freq_ht = hl.read_table("gs://gnomad/v4.0/sample_qc/exomes/gnomad.exomes.v4.0.f_stat_sites.ht")
sex_ht = annotate_sex(vds, included_intervals=calling_intervals, sites_ht=freq_ht, f_stat_cutoff=-1, aaf_expr="AF", gt_expr="LGT", use_gaussian_mixture_model=True)
sex_ht2 = annotate_sex(mt, included_intervals=calling_intervals, sites_ht=freq_ht, f_stat_cutoff=-1, aaf_expr="AF", gt_expr="LGT", use_gaussian_mixture_model=True)
sex_ht3 = annotate_sex(vds, included_intervals=calling_intervals, sites_ht=freq_ht, f_stat_cutoff=-1, aaf_expr="AF", gt_expr="LGT", use_gaussian_mixture_model=True, variants_only_x_ploidy=True)
sex_ht4 = annotate_sex(mt, included_intervals=calling_intervals, sites_ht=freq_ht, f_stat_cutoff=-1, aaf_expr="AF", gt_expr="LGT", use_gaussian_mixture_model=True, variants_only_x_ploidy=True)

show(hl.plot.scatter(sex_ht.chrX_ploidy, sex_ht.chrY_ploidy, label=sex_ht.sex_karyotype))
show(hl.plot.scatter(sex_ht2.chrX_ploidy, sex_ht2.chrY_ploidy, label=sex_ht2.sex_karyotype))
show(hl.plot.scatter(sex_ht3.chrX_ploidy, sex_ht3.chrY_ploidy, label=sex_ht3.sex_karyotype))
show(hl.plot.scatter(sex_ht4.chrX_ploidy, sex_ht4.chrY_ploidy, label=sex_ht4.sex_karyotype))

[klaricch]

is this in general the names we want to use or it is based on the reference used?

[jkgoodrich]

This is what we used for UKBB and v3, so I was keeping the output consistent since this function was used in both of those repos

[klaricch]

lgtm