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document changes for minimap2 support #7

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Mar 29, 2023
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document changes for minimap2 support #7

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8 changes: 8 additions & 0 deletions CHANGELOG.md
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# 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
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20 changes: 19 additions & 1 deletion docs/quickstart.md
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# User Guide
Table of contents:

* [Quickstart](#quickstart)
* [Supported upstream processes](#supported-upstream-processes)
* [Output files](./outputs.md)

# Quickstart
```
hificnv \
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These tracks visualized in IGV appear as follows:

![](../img/hg002_chr7_tracks.png)
![](../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.