DeepVariant 1.6.0

• Improved support for haploid regions, chrX and chY. Users can specify haploid regions with a flag. Updated case studies show usage and metrics.
• Added pangenome workflow (FASTQ-to-VCF mapping with VG and DeepVariant calling). Case study demonstrates improved accuracy
• Substantial improvements to DeepTrio de novo accuracy by specifically training DeepTrio for this use case (for chr20 at 30x HG002-HG003-HG004, false negatives reduced from 8 to 0 with DeepTrio v1.4, false positives reduced from 5 to 0).
• We have added multi-processing ability in postprocess_variants which reduces 48 minutes to 30 minutes for Illumina WGS and 56 minutes to 33 minutes with PacBio.
• We have added new models trained with Complete genomics data, and added case studies.
• We have added NovaSeqX to the training data for the WGS model.
• We have migrated our training and inference platform from Slim to Keras.
• Force calling with approximate phasing is now available.

We are sincerely grateful to

• @wkwan and @paulinesho for the contribution to helping in Keras move.
• @lucasbrambrink for enabling multiprocessing in postprocess_variants.
• @MSamman, @akiraly1 for their contributions.
• PacBio: William Rowell (@williamrowell), Nathaniel Echols for their feedback and testing.
• UCSC: Benedict Paten(@benedictpaten), Shloka Negi (@shlokanegi), Jimin Park (@jimin001), Mobin Asri (@mobinasri) for the feedback.