How to prepare vcf file for Duplication & Tandem Duplication? about paragraph

[traxexx]

Hi Zhiliang,

In real practice Paragraph treats duplications as insertions. With such treatment, the similarity between duplications can significant lower the genotyping performance. And for large DUPs (the one at 1:2388494), the best genotyping method should be read depth counting, but it's not in Paragraph current version yet. Let me check if there is any other good solutions for this case.

[traxexx]

For now maybe try GenomeStrip for CNVs? It should work for both discovery and genotyping mode:
http://software.broadinstitute.org/software/genomestrip/
It will work better if you have a bunch of samples running together.

[Zhiliang-Zhang]

For now maybe try GenomeStrip for CNVs? It should work for both discovery and genotyping mode:
http://software.broadinstitute.org/software/genomestrip/
It will work better if you have a bunch of samples running together.

Hi,
Thanks for your reply and advice. That sounds great and I will have a try.

Zhiliang