Make artifical variants(SNVs/InDels))
- Split FASTA into seperate files by chromsome (ex, chr1.fa)
- Python library (requirements.txt)
- pandas
- numpy
- HTSeq
git clone https://github.com/hongiiv/artifical_variants.git
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)