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Simulating SV in PacBio reads #184
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Hi , Hope that helps |
I want to create structural variants in the downloaded PacBio data and run it in sv detection pipeline and see if the variant is detected. Is this possible Thank you |
yes, see here https://github.com/fritzsedlazeck/SURVIVOR/wiki#quick-start |
Thank you. I have to replace the reference.fasta with the dwonloaded fasta file. Is this right?. |
please read the instructions. you need to change the one option 0 to 1 . |
Thank you. So, I did these steps: Simulated the structural variations in the reference genome using the parameters given in package:
Then simulated the reads using simlord:
I ran it in my SV detection_workflow and there were no structural variants in vcf file. Is this because of the low number of reads generated? Thank you |
Hello
I need some suggestions in simulating complex structural variants in Hifi reads file from PacBio
https://downloads.pacbcloud.com/public/dataset/HG002-CpG-methylation-202202/m64011_190830_220126.hifi_reads.bam
I could understand from the wiki page that SVs can be created in the reference genome. How to simulate these variants in a file that I am interested in.
Thank you
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