diff --git a/CHANGELOG.md b/CHANGELOG.md index 3bdc016..d225f98 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # Change Log +## v0.1.6 - 2023-03-29 +### Additions +* Added support for minimap2-aligned BAM files +* Updated quickstart to specify supported upstream tools + +### Fixed +* Improved error messaging for cov-regex mismatch + ## v0.1.5 - 2023-03-14 ### Fixed * Adjust linux release build process to improve portability diff --git a/docs/quickstart.md b/docs/quickstart.md index 825c1ff..c653a86 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -1,3 +1,10 @@ +# User Guide +Table of contents: + +* [Quickstart](#quickstart) +* [Supported upstream processes](#supported-upstream-processes) +* [Output files](./outputs.md) + # Quickstart ``` hificnv \ @@ -55,4 +62,15 @@ HG002_male.HG002.copynum.bedgraph HG002_male.HG002.depth.bw HG002_male.HG002.m These tracks visualized in IGV appear as follows: -![](../img/hg002_chr7_tracks.png) \ No newline at end of file +![](../img/hg002_chr7_tracks.png) + +# Supported upstream processes +The following upstream processes are supported as inputs to HiFiCNV: + +* Aligners (BAM files): + * [pbmm2](https://github.com/PacificBiosciences/pbmm2) (recommended) + * [minimap2](https://github.com/lh3/minimap2) +* Variant callers (for MAF) + * [DeepVariant](https://github.com/google/deepvariant) - for SNV/indel + +Other upstream processes may work with HiFiCNV, but there is no official support for them at this time.