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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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Running SVTyper on any SV tool #85

Open mej54 opened 6 years ago

mej54 commented 6 years ago

Hi,

I'm hoping to be able to run SVTyper in a generic mode on any SV tool.

I have tried running SVTyper on Manta and SvAbA vcfs, and am running into errors because SVTyper is looking for information that is not listed in these files. For example, some entries in Manta do not have CIPOS and SvAbA does not list CIPOS for any of its entries. SVTyper stops and throws an error because it cannot find CIPOS. There have also been other format-specific errors I've run into, such as SVTyper throwing an error when an additional '>' is found in the FORMAT header section.

Will there be a version of SVTyper that is more lenient with the vcf format, so that it can be run on other SV callers besides Lumpy?

slzarate commented 6 years ago

I have also tried running svtyper_sso on CNVnator and BreakSeq VCFs, and I am running into the same error.

ytguojian commented 6 years ago

Hi Molly, Have you resolved that problem? I am facing the same problem.

ernfrid commented 6 years ago

I think there is likely to be a version of svtyper that does this at some point, but I'm not sure when that may happen. I've run into the same issue for Manta and have had to add CIPOS and CIEND manually using bcftools.

mej54 commented 6 years ago

Ok, thank you for the update!

janawold1 commented 3 years ago

I know this is an old issue, but is there a standardised way to decide how to bound CIPOS and CIEND? Is it a proportion of the overall size of the SV?

dmckean commented 3 years ago

111 works around the missing CIPOS

dr-ashu-geno commented 2 years ago

Dear @ernfrid

I know this is a very old issue; but may I ask how you added CIPOS and CIEND using bcftools? Any specific commands? Can bcftools calculate these CIs for SVs?

Thank you in advance

ernfrid commented 2 years ago

@dr-ashu-geno - It's been too long for me to recall for certain, but I'm fairly sure I calculated outside of svtools and then simply added the new tags to the VCF using bcftools annotate. I'm not aware of a standard way to calculate these. I know in the past I used either fixed window sizes or 0 size, but that was tool dependent.