Version 1.1 ___________ 1.1.0 ----- This version adds a host of new features to pVACtools: - pVACseq is now able to parse VAF, depth, and expression information directly from the VCF. This makes the ``--additional-input-file-list`` option obsolete. The ``--additional-input-file-list`` option is now deprecated and will be removed in an upcoming release. For more information on how to annotate your VCF with readcount and expression information, see the :ref:`prerequisites_label` page. - pVACseq is now able to handle proximal germline and somatic variants. In order to incorporate those into the epitope predictions, you will need to provide a phased variants VCF to your pVACseq run using the ``--phased-proximal-variants-vcf`` option. For more information on how to create this file, see the :ref:`prerequisites_label` page. - We added support to pVACseq for filtering on transcript support levels. This requires the input VCF to be annotated with the TSL field by VEP. Be default, any transcripts with a TSL above 1 will be filtered out. - The binding filter of pVACseq and pVACfuse can now be run with flexible, allele-specific binding-thresholds. This feature can be enabled using the ``--allele-specific-binding-thresholds`` flag. The thresholds used are taken from `the IEDB recommendations `_. - pVACseq now supports a ``--pass-only`` flag that will result in any VCF entries with a ``FILTER`` to be skipped. Using this flag, only VCF entries with a ``FILTER`` of ``PASS`` or ``.`` will be processed. - We added support for the `MHCflurry `_ and `MHCnuggets `_ prediction algorithms. These can be used by listing ``MHCflurry``, ``MHCnuggetsI`` (for MHC Class I alleles), and/or ``MHCnuggetsII`` (for MHC Class II alleles) as the prediction algorithms in your run commands. - The default ``--tdna-vaf`` and ``--trna-vaf`` cutoff values have been updated from 0.4 to 0.25. This is the minimum VAF threshold that an epitope candidate must meet in order to pass the coverage filter. - We now offer a graphical user interface, pVACviz, to run pVACseq as an alernative to using the command line. pVACviz, can also be used to plot and filter your pVACseq results. 1.1.1 ----- This is a hotfix release. It fixes the following issue(s): - In version 1.1 we updated VAFs to be fractions, rather than percentages. A bug in this code change resulted in an error when using custom VAF cutoff values instead of the default. This has now been fixed. 1.1.2 ----- This is a hotfix release. It fixes the following issue(s): - In version 1.1.0 we added a ``--pass-only`` flag to pVACseq that would result in only variants with ``FILTER`` of ``PASS`` or ``.`` getting processed. However, this option was not getting passed along to the pVACseq process correctly, resulting in this option not taking effect. This hotfix release fixes this issue and the ``--pass-only`` flag should now work as expected. 1.1.3 ----- This is a hotfix release. It fixes the following issue(s): - When using the MHCnuggets prediction algorithm for MHC class II alleles (``MHCnuggetsII``) not all epitope sequences were predicted for inframe insertions. This issues has now been fixed. - For MHCflurry, cases with peptide sequences that were shorter than the desired epitope length were not handled correctly which resulted in an error. This issue has been resolved in this release. 1.1.4 ----- This is a hotfix release. It fixes the following issue(s): - When running pVACvector with a with a pVACseq input file and the corresponding VCF, the sample name wasn't being passed along correctly which would cause an error if the input VCF was a multi-sample VCF. - pVACseq would throw an error if the value of a gene or transcript expression field was empty. 1.1.5 ----- This is a hotfix release. It fixes the following issue(s): - When running pVACseq with a phased input VCF the mutation position offset of a frameshift somatic variant to their proximal variants was not getting calculated correctly, leading to errors. - For running pVACvector we removed a dependency on a commandline tool by using a python library instead. This allowed us to remove a system call to a tool that required standalone installation by the user.