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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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Identifying variants from de novo assembly files #595

Closed priyambial123 closed 1 year ago

priyambial123 commented 1 year ago

Hello,

I referred to the PBSV documentation https://github.com/PacificBiosciences/pbsv and could see that aligned bam file was used to identify structural variation signatures. So, using the bam file from Hifiasm (de novo assembly step), I ran the next step:

pbsv discover 002-082.asm.GRCh38.bam 002-082.svsig.gz

FATAL RUN 0X2ab3e70c8340. pbsv discover ERROR: Hard clips are not supported

Is there a way to identify the structural variants from de novo assembled files (hifiasm)

Thank you

Priya

armintoepfer commented 1 year ago

You need to remove cigars H from your alignments. I bet there are tools are scripts available.