dnanexus-rnd / GLnexus / 2030

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travis-ci

Add --more-PL option to propagate PL from reference bands (#180)

The --more-PL flag causes glnexus_cli to fill in all PL vectors in the output pVCF.

1. The PL for 0/0 entries are populated from reference bands.
2. PL entries for genotypes including alleles not present in a given sample gVCF are populated from the sample PL using the gVCF symbolic allele (<*> or <NON_REF>)
3. Any other entries that can't be filled safely are set to 0 or 999 as appropriate, instead of the VCF missing value (.).

The new mode is slower and inflates the pVCF output size, often for limited useful information added, compared to the default mode which omits these cases. However, it can provide compatibility with downstream programs which require 100% of PL values filled in (e.g. Beagle gl= imputation).

The command-line flag sets genotyper_config::more_PL to true.

99 of 99 new or added lines in 3 files covered. (100.0%)

4289 of 4593 relevant lines covered (93.38%)

952866.0 hits per line