Simulating SV in PacBio reads

[priyambial123]

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

[fritzsedlazeck]

Hi ,
so just to get this right, you want to simulate SV and use real reads? This is also based on the reference option. There is an option which way you want to simulate. In this case you would need to map the real reads to the so modified reference.

Hope that helps
Fritz

[priyambial123]

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

[fritzsedlazeck]

yes, see here https://github.com/fritzsedlazeck/SURVIVOR/wiki#quick-start
change the options as described in the text.

[priyambial123]

Thank you. I have to replace the reference.fasta with the dwonloaded fasta file. Is this right?.

[fritzsedlazeck]

please read the instructions. you need to change the one option 0 to 1 .
and then remap your reads to the newly generated fasta file

[priyambial123]

Thank you. So, I did these steps:

Simulated the structural variations in the reference genome using the parameters given in package:

./SURVIVOR simSV "/SURVIVOR/Debug/human_GRCh38_no_alt_analysis_set.fasta" "/SV_tools/SURVIVOR/Debug/parameter_file" 0.1 0 simulated

Then simulated the reads using simlord:

simlord --read-reference/SV_tools/SURVIVOR/Debug/simulated.fasta -n 10000 myreads

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