Help with MEI annotation

[fjmuzengyiheng]

Hi, SCRAMBLE is such a first-tier tool for MEI detection.
Can output txt file be converted into VCF file for further gene-based annotation or 1000G frequency annotation(dbRIP) ?
Thank you!

[rebeccaito]

Thanks for your comment. I am working on this improvement. I hope to add Scramble deletion calling and VCF outputs in the next week or so.

[fjmuzengyiheng]

Thank you for your great work!

[rebeccaito]

scramble should be able to write to VCF now if you provide a reference fasta file, please test and let me know if it works for you

[fjmuzengyiheng]

THANKS, I will test it as soon as possible.

[Bin-Guan]

Our installation for the version 1.0.1 finished MEI detection and deletion detection, generated two txt files. However, it gave the following error when writing the vcf file. Using the test data provided did generate the vcf file. For our own data, we're using the reference file human_g1k_v37_decoy.fasta, which has contigs GL000220.1and hs37d5. Alternatively, could you add an argument to turn off VCF?
Error:
Error in if (nrow(fixed) > 0) { : argument is of length zero
Calls: write.scramble.vcf
Execution halted