For joint variant calling, produce a final VCF file with filtered variants (those that PASS filters)

[amizeranschi]

Description of feature

Following this discussion on Slack, after running joint calling and VQSR, it would be helpful to produce a final VCF file with filtered variants, i.e. those that have PASS on their filter column, and not . or anything else. Something like the following bcftools command:

bcftools view -f PASS joint_germline_recalibrated.vcf.gz > joint_germline_recalibrated_final.vcf.gz

The current behavior is to have a mix of both calibrated and uncalibrated variants in joint_germline_recalibrated.vcf.gz, which means that there are two records for each variant.