Straglr conversion support to json for MAVIS annotation

[sarahdada]

Hello!

I am using Straglr (https://github.com/bcgsc/straglr) for analysis long-read sequencing tandem repeats. The output of the tool is .tsv and .bed . I wanted to annotate the .tsv.

The .bed has the header : #chrom start end repeat_unit allele1:size allele1:copy_number allele1:support allele2:size allele2:copy_number allele2:support.

The .tsv is the version that would be more useful for annotation, that I was hoping could be converted to json format for MAVIS annotation. The headers are : #chrom start end repeat_unit genotype read copy_number size read_start allele

THANK YOU!
Sarah!

[zhemingfan]

Hi @sarahdada, can you post a sample input with a few rows?

[sarahdada]

yes! sorry one second here

[creisle]

@sarahdada what version of straglr were you using here?

[sarahdada]

Sorry, whatever is literally on the front page of the straglr github! Quick start.

[sarahdada]

Titled : Final release before publication