HaloPlex pipeline: changed N-masking of initial parts of reads to soft clipping. This avoids underestimation of QD (qualty by depth).
HaloPlex pipeline: added alternative recipe for variant calling, not using the merged VCF file but instead the individual BAMs. Creating the merged VCF can take very long (e.g. 16h on 1 core for a project with 196 samples sequenced on 2 flow cells; the command cannot be parallelized). This new alternative recipe provides a faster route (for the same example: 2.5h on 16 cores for variant calling from individual files, compared to 1h using the merged file).