DeepVariant 1.3.0

• Improved the DeepTrio PacBio models on PacBio Sequel II Chemistry v2.2 by including this data in the training dataset.
• Improved call_variants speed for PacBio models (both DeepVariant and DeepTrio) by reducing the default window width from 221 to 199, without tradeoff on accuracy. Thanks to @lucasbrambrink for conducting the experiments to find a better window width for PacBio.
• Introduced a new flag --normalize_reads in make_examples, which normalizes Indel candidates at the reads level.This flag is useful to reduce rare cases where an indel variant is not left-normalized. This feature is mainly relevant to joint calling of large cohorts for joint calling, or cases where read mappings have been surjected from one reference to another. It is currently set to False by default. To enable it, add --normalize_reads=true directly to the make_examples binary. If you’re using the run_deepvariant one-step approach, add --make_examples_extra_args="normalize_reads=true". Currently we don’t recommend turning this flag on for long reads due to potential runtime increase.
• Added an --aux_fields_to_keep flag to the make_examples step, and set the default to only the auxiliary fields that DeepVariant currently uses. This reduces memory use for input BAM files that have large auxiliary fields that aren’t used in variant calling. Thanks to @williamrowell and @rhallPB for reporting this issue.
• Reduced the frequency of logging in make_examples as well as call_variants to address the issue reported in #491.