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Update documentation
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nicolaasuni committed Nov 22, 2018
1 parent da05e00 commit 68a8f82
Showing 13 changed files with 51 additions and 36 deletions.
2 changes: 1 addition & 1 deletion VERSION
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@@ -1 +1 @@
5.3.4
5.3.5
2 changes: 1 addition & 1 deletion c/doc/Doxyfile
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@@ -32,7 +32,7 @@ PROJECT_NAME = "VariantKey"
# This could be handy for archiving the generated documentation or
# if some version control system is used.

PROJECT_NUMBER = 5.3.4
PROJECT_NUMBER = 5.3.5

# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer
2 changes: 1 addition & 1 deletion conda/c.src/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: variantkey-src
version: 5.3.4
version: 5.3.5

source:
path: ../..
2 changes: 1 addition & 1 deletion conda/c.vk/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: variantkey-vk
version: 5.3.4
version: 5.3.5

source:
path: ../..
8 changes: 4 additions & 4 deletions conda/python-class/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: pyvariantkey
version: 5.3.4
version: 5.3.5

source:
path: ../..
@@ -14,11 +14,11 @@ requirements:
- setuptools
- numpy >=1.15.0
build:
- variantkey >=5.3.4
- variantkey >=5.3.5
- numpy >=1.15.0
run:
- python
- variantkey >=5.3.4
- variantkey >=5.3.5
- numpy >=1.15.0

test:
@@ -30,7 +30,7 @@ test:
- pytest-cov
- pytest-benchmark
- pycodestyle
- variantkey >=5.3.4
- variantkey >=5.3.5
- numpy >=1.15.0
imports:
- pyvariantkey
2 changes: 1 addition & 1 deletion conda/python/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: variantkey
version: 5.3.4
version: 5.3.5

source:
path: ../..
2 changes: 1 addition & 1 deletion conda/r/meta.yaml
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@@ -1,6 +1,6 @@
package:
name: r-variantkey
version: 5.3.4
version: 5.3.5

source:
path: ../..
4 changes: 2 additions & 2 deletions python-class/setup.py
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@@ -33,7 +33,7 @@ def run(self):

setup(
name='pyvariantkey',
version='5.3.4.1',
version='5.3.5.1',
keywords=('variantkey variant key genetic genomics'),
description="VariantKey Python wrapper class",
long_description=read('../README.md'),
@@ -51,7 +51,7 @@ def run(self):
],
install_requires=[
'numpy>=1.15.0',
'variantkey>=5.3.4.1',
'variantkey>=5.3.5.1',
],
extras_require={
'test': [
2 changes: 1 addition & 1 deletion python/setup.py
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@@ -30,7 +30,7 @@ def run(self):

setup(
name='variantkey',
version='5.3.4.1',
version='5.3.5.1',
keywords=('variantkey variant key genetic genomics'),
description="VariantKey Bindings for Python",
long_description=read('../README.md'),
2 changes: 1 addition & 1 deletion r/variantkey/DESCRIPTION
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@@ -1,6 +1,6 @@
Package: variantkey
Title: Genetic VariantKey
Version: 5.3.4.1
Version: 5.3.5.1
Authors@R: person("Nicola", "Asuni", email = "info@genomicsplc.com", role = c("aut", "cre"))
Description: Tools to generate and process a 64 bit Unsigned Integer Keys for Human Genetic Variants.
The VariantKey is sortable for chromosome and position,
49 changes: 32 additions & 17 deletions resources/tools/README.md
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# VCFNORM

Script and tools to normalize VCF files.

## Normalization process:

* Replace the Genome reference with the one manually set (e.g. GRCh37.p13.b146)

* [Decompose](https://genome.sph.umich.edu/wiki/Vt#Decompose) multiallelic variants in a VCF file. If the VCF file has genotype fields GT,PL, GL or DP, they are modified to reflect the change in alleles. All other genotype fields are removed.

* [Normalize](https://genome.sph.umich.edu/wiki/Vt#Normalization) variants as in [Tan et al. 2015](https://academic.oup.com/bioinformatics/article/31/13/2202/196142).

* Extend the VCF file to include [VariantKey](https://github.com/Genomicsplc/variantkey) fields.

* Compress and index the VCF file.

* Generate RSID to VariantKey binary files.
# Tools

Scripts to normalize VCF files and generate VariantKey information.


* **fastabin.sh**
* Create a binary version of the input reference genome sequence FASTA file for quick lookup.
It only extract the first 25 sequences for chromosomes 1 to 22, X, Y and MT.

* **vcfnorm.sh**
* Normalize VCF files (allele decomposition + normalization)
* *Requires*:
* vt (https://github.com/atks/vt)
* tabix

* **vkhexbin.sh**
* Process the variantKey HEX file to generate the final binary counterparts:
* <FILE>.vcf.gz : decomposed and normalized VCF file with added VariantKey.
* <FILE>.vcf.gz.tbi : VCF file index.
* vkrs.bin : VariantKey to rsID binary lookup table.
* rsvk.bin : rsID to VariantKey binary lookup table.
* nrvk.bin : Non-reversible VariantKey to REF+ALT lookup table.
* *Requires*:
* vt (https://github.com/atks/vt)
* bcftool (https://github.com/samtools/bcftools/tree/develop)
* sort (coreutils)
* xxd (vim-common)

## NOTE:

Prebuilt binary files can be downloaded from:
https://sourceforge.net/projects/variantkey/files/
2 changes: 1 addition & 1 deletion resources/tools/vcfnorm.sh
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@@ -5,7 +5,7 @@
# Normalize VCF files (allele decomposition + normalization)
#
# Requires:
# - vt
# - vt (https://github.com/atks/vt)
# - tabix
#
# On Debian/Ubuntu:
8 changes: 4 additions & 4 deletions resources/tools/vkhexbin.sh
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@@ -8,10 +8,10 @@
# - nrvk.bin : Non-reversible VariantKey REF+ALT map
#
# Requires:
# - vt
# - bcftoolsvh (Genomics PLC version of bcftools)
# - sort (coreutils)
# - xxd (vim-common)
# - vt (https://github.com/atks/vt)
# - bcftool (https://github.com/samtools/bcftools/tree/develop)
# - sort (coreutils)
# - xxd (vim-common)
#
# On Debian/Ubuntu:
# sudo apt-get update && sudo apt-get install -y --allow-unauthenticated vt bcftoolsvh tabix coreutils vim-common

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