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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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questions about pbsv #671

Closed rabbitdsy closed 3 months ago

rabbitdsy commented 6 months ago

I have 180 samples, and I used “Parallel processing per chromosome” pipeline, and obtained ".svsig.gz" file for each sample. I have tried to joint call all samples together (CHM2.0 as ref) using "pbsv call -j 40 T2T.fa T2T.sample1.*.svsig.gz T2T.sample1.vcf", but it took too long (40 cores 128 GB). I wonder can I call SV for each sample separately, and get one-sample vcf, and then merge all vcf together? If can, what is the differences between "separately calling and merge" vs "joint calling"?

Waiting for your suggestions, Thanks

armintoepfer commented 3 months ago

Hi. You can do the either. Yes it will take very long to jointly call 180 samples. It's a philosophical question about your approach that only you can answer.