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incorporateVCF
chrismit edited this page Feb 12, 2014
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The script incorporateVCF will implement the variants of a VCF file into a fasta file. Here is an example usage:
python pythomics/scripts/incorporateVCF.py --vcf /media/chris/masterVar2VCF_rev1_ShanYang/masterVar.vcf --append-chromosome -f /home/chris/ref/human/hg19.fa --heterozygous --individual 1 > /home/chris/hg19_with_all_snps.fasta
python pythomics/scripts/incorporateVCF.py --vcf /media/chris/masterVar2VCF_rev1_ShanYang/masterVar.vcf --append-chromosome --dels --ins -f /home/chris/ref/human/hg19.fa --heterozygous --individual 1 > /home/chris/hg19_with_all_variants.fasta