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Artifical Variants

Build Status codecov CRAN status lifecycle License: MIT made-with-python GitHub issues

Make artifical variants(SNVs/InDels))

Prerequisites

  • Split FASTA into seperate files by chromsome (ex, chr1.fa)
  • Python library (requirements.txt)
  • pandas
  • numpy
  • HTSeq

Install

git clone https://github.com/hongiiv/artifical_variants.git

Run

BRCA1 all missense mutations and ±100 bp intron. All BRCA1 transcripts are collapse intervals.

$ python artifical_variants.py brca1.txt 17 brca1_artifical.vcf /NGENEBIO/workflow-dependencies/seqseek/homo_sapiens_GRCh37/chr17.fa

BRCA2

$ python artifical_variants.py brca2.txt 13 brca2_artifical.vcf /NGENEBIO/workflow-dependencies/seqseek/homo_sapiens_GRCh37/chr13.fa

$ python artifical_variants.py --help
usage: artifical_variants.py [-h] [--vartype {SNV,INS,DEL}]
                             input_transcript chrom output_vcf ref

Run make artifical variants(SNVs/InDels)

positional arguments:
  input_transcript      Transcript file(ex, brca1.txt)
  chrom                 Chromosome number(ex, 17)
  output_vcf            Output vcf file (ex, brca1_artifical.vcf)
  ref                   Spliting FASTA file by chromosome

optional arguments:
 -h, --help            show this help message and exit
 --vartype {SNV,INS,DEL}
                      Type of variant (default: SNV)

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