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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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Running RetroSeq on heterozygous data #11

Closed jacau closed 5 years ago

jacau commented 7 years ago

I'm using the latest version RetroSeq (1.5) and when I run -call with -hets I get an error that it's not a valid option. Is the latest version altered to handle heterozygous data by default?

oiiio commented 6 years ago

About a year later, I am having this same question. The hets seem to be handled in code, but the README still mentions the parameter and it would be nice to have an answer from the author

afadda91 commented 6 years ago

same question. still no answer?

tk2 commented 5 years ago

Hi - yes, the later versions will detect het calls by default. Apologies for the late reply.