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MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
135 stars 28 forks source link

Output variant sequences #14

Closed CWYuan08 closed 5 years ago

CWYuan08 commented 5 years ago

Hi Maria, I am wondering whether it is possible to get the variant sequences, so that I can compare them to variants called by a different software.

Thank you very much Ulrika

MariaNattestad commented 5 years ago

Hi Ulrika

Unfortunately the input file that Assemblytics takes (a delta file) doesn't include the sequences so Assemblytics can't do this automatically for you. However, there is a great way to do it by using the output bed file from Assemblytics and running it against your fasta file using bedtools fastaFromBed: https://bioweb.pasteur.fr/docs/modules/bedtools/2.17.0/content/fastafromBed.html

Hope that helps! Maria