GATK uses two different approaches for site-level variant filtration:
1) Hard filtering
2) VQSR. See here
Currently, the pipeline uses hard filtering only but VQSLOD is generated by VQSR method (VariantRecalibrator and ApplyVQSR). There should be an option to choose which method for variant filtering.
(VQSR method generated VQSLOD is needed by dEploid deconvolution.)
GATK uses two different approaches for site-level variant filtration: 1) Hard filtering 2) VQSR. See here
Currently, the pipeline uses hard filtering only but VQSLOD is generated by VQSR method (VariantRecalibrator and ApplyVQSR). There should be an option to choose which method for variant filtering.
(VQSR method generated VQSLOD is needed by dEploid deconvolution.)