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Identify variants (snv, indel, sv) by mapping reads onto the reference.

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Name		Name	Last commit message	Last commit date
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bin		bin
scripts		scripts
test		test
.gitignore		.gitignore
LICENSE		LICENSE
README.MD		README.MD
environment.yml		environment.yml

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Identify variants by mapping reads onto the reference

Install

use the conda environment by

conda env create --prefix=edit -f environment.yml
conda activate edit

or install these tools and add them to system path

samtools
bwa
freebayes
svaba

Test

cd test/
sh test.sh

Run

python map_variant.py -h

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Identify variants (snv, indel, sv) by mapping reads onto the reference.

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