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vcf2fasta

reference fasta to diploid fasta via SNPs in VCF

Usage


$ python scripts/vcf2fasta.py --help
usage: vcf2fasta.py [-h] -r REF_FASTA -v VCF_FILE -n NAME [--verbose]
                    [--version]

vcf2fasta (diploid)

optional arguments:
  -h, --help            show this help message and exit
  -r REF_FASTA, --ref REF_FASTA
                        input reference file (fasta) (default: None)
  -v VCF_FILE, --vcf VCF_FILE
                        input vcf file (vcf) (default: None)
  -n NAME, --name NAME  sample name (column header) (default: None)
  --verbose             Increase verbosity (specify multiple times for more)
                        (default: None)
  --version             show program's version number and exit

Usage Examples


python scripts/vcf2fasta.py -r test/dm3__chr2L.fa.gz -v test/DGRP-057.vcf -n DGRP-057
python scripts/vcf2fasta.py -r test/dm3__chr2L.fa.gz -v test/DGRP-057.vcf -n DGRP-057 --verbose

Change Log

Bugs and Feedback

For bugs, questions and discussions please use the Github Issues.

LICENSE

Licensed under the Apache License, Version 2.0 (the 'License'); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an 'AS IS' BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.