vcf2revcom.pl - No modifications to the fasta and gtf file about snpgenie

[singing-scientist]

Thanks for using SNPGenie, and apologies that I lost track of this! Those instructions refer to the script in the other repository. For the vc2revcom script at the SNPGenie page, please run as follows:

vcf2revcom.pl <file_name>.vcf <seq_length>

Thus, you will also need to know the total length of your sequence as well. Let me know if that works as expected for you, and if so, we can move on to revcom for GTF and FASTA.

Please let me know if this works! If not, please share a sample file so I may troubleshoot.

[lchallagundla]

I did convert the Snp report as per the instructions with the length of the fasta file. My question still relates to how are you reverse complementing the gtf and reference fasta.
Thanks.

[singing-scientist]

Coordinates can be reverse-complemented simply as length - position + 1, and the reverse complement of FASTA files can be found by reversing the sequence and replacing A>T, C>G, G>C, and T>A. I now provide scripts to do this, which can be run as follows — apologies that I have not yet had time to document them.

gtf2revcom.pl <file_name>.gtf <seq_length>
fasta2revcom.pl <seq>.fa

Let me know if those work!

[lchallagundla]

Great. I will try these and let you know if they work!
Thanks.