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NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
https://www.nature.com/articles/s41598-018-23978-z
MIT License
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Convert output to VCF / get reference allele #3

Closed thedam closed 4 years ago

thedam commented 6 years ago

Hi, I'd like to convert IMSindel output to VCF-like format. VCF contains fields: chr, start_pos, whateverID, ref_allel, alt_allel and IMSindel only gives: chr, sttpos, indel_str

How to determine ref_allel?

is it enough to make a trick: samtools faidx ref.fa chr:sttpos-sttpos samtools faidx ref.fa 1:13657-13657 or maybe you could modify the code to output this :)

Thanks for advice!:) Damian

holrock commented 6 years ago

We are planning VCF support in a future release. Please use that workaround now. Thanks!