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5.3.4 | ||
5.3.5 |
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package: | ||
name: variantkey-src | ||
version: 5.3.4 | ||
version: 5.3.5 | ||
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source: | ||
path: ../.. | ||
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package: | ||
name: variantkey-vk | ||
version: 5.3.4 | ||
version: 5.3.5 | ||
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source: | ||
path: ../.. | ||
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package: | ||
name: variantkey | ||
version: 5.3.4 | ||
version: 5.3.5 | ||
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source: | ||
path: ../.. | ||
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package: | ||
name: r-variantkey | ||
version: 5.3.4 | ||
version: 5.3.5 | ||
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source: | ||
path: ../.. | ||
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# VCFNORM | ||
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Script and tools to normalize VCF files. | ||
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## Normalization process: | ||
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* Replace the Genome reference with the one manually set (e.g. GRCh37.p13.b146) | ||
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* [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. | ||
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* [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). | ||
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* Extend the VCF file to include [VariantKey](https://github.com/Genomicsplc/variantkey) fields. | ||
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* Compress and index the VCF file. | ||
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* Generate RSID to VariantKey binary files. | ||
# Tools | ||
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Scripts to normalize VCF files and generate VariantKey information. | ||
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* **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. | ||
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* **vcfnorm.sh** | ||
* Normalize VCF files (allele decomposition + normalization) | ||
* *Requires*: | ||
* vt (https://github.com/atks/vt) | ||
* tabix | ||
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* **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) | ||
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## NOTE: | ||
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Prebuilt binary files can be downloaded from: | ||
https://sourceforge.net/projects/variantkey/files/ |
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