Hi everyone,
I am trying to call for structural variants (using svim) in my PacBio long reads sequencing dataset. However, I noticed that I get a vastly different number of variants (100,000 vs 1,000) when I used a bam alignment (from ngmlr) directly converted with samtools versus one that I processed with samtools fixmate and samtools markdup prior (significantly less in the latter). (Workflow: https://www.htslib.org/workflow/fastq.html)
Is this normal? And are these steps necessary for this specific use case (SV calling)? (Frankly I do not quite understand what impact the samtools fixmate or samtools markdup might be)
Thank you very much for your help.
[Edited for clarity]
Best regards,
ZH
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written
by
Zeng Hao •
1 answer
I do not think samtools fixmate and markdup are going to work on PacBio long reads. fixmate is for setting and repairing mate information for read pairs which (as far as I know) PacBio does not have. markdup might do something useful with the right settings, but I do not know if anyone has ever tried it properly.
If they are not helping you then I would not use them.
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