Run the aligned files from different smrtcells

[priyambial123]

Hello

I need a suggestion on running the structural variant calling on hifi data from two SMRT cells. I have two aligned bam files from same subject (run in 2 smart cells, PacBio). I tried doing the variant call for aligned file from each SMRT cell. Then sorted the vcf from each smrt cell but creating index for the vcf fails. Can you suggest a way to run aligned files from different smrt cells and create a single vcf file

Thank you

[tjiangHIT]

Hello @priyambial123,

I want to confirm that these two alignment files are from two SMRT cells both belong to the same sample, is that correct?
If so, I suggest you merge the two alignment files into one file via Samtools and then perform cuteSV to complete SV calling.
In this way, cuteSV will provide a single vcf file for your further analysis.
Hope this can help you.

Tao

[priyambial123]

Thank you, yes it worked after merging, sorting and indexing the bam files. Is joint variant calling possible using cuteSV?

[tjiangHIT]

Please perform the following steps to achieve joint SV calling:

1. Run cuteSV for each sample to generate sample specific SV callsets.
2. Perform SURVIVOR to merge every single vcf into merged.vcf.
3. Rerun cuteSV for each sample with -Ivcf merged.vcf (force calling step).
4. Perform SURVIVOR again to merge every force called single vcf into final_merged.vcf.

Hope this can help you.
Tao