d-cameron
commented
1 year ago We have successfully used gridss on BGI data in the past.
All gridss calls are in breakend notation - this is expected behaviour. See https://github.com/PapenfussLab/gridss#why-are-all-calls-bnd for details.
On Mon, 19 Dec 2022, 19:36 DomManou, @.***> wrote:
Hello,
I would like to run GRIDSS for SV calling on short-read sequencing data. However, my dataset is not produced through Illumina technologies (DNBseq-BGI). To "test the waters", I ran GRIDSS on a test sample. Although the software runs, the output .vcf file contains only "SVTYPE=BND".
I am wondering whether the vcf output reflects an issue arising from the sequencing output. If so, have you found/could there be a way to adjust the software for non-illumina sequencing output (e.g. through SAMtags etc)? Any help is greatly appreciated :)
Best regards, Domniki
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Hello,
I would like to run GRIDSS for SV calling on short-read sequencing data. However, my dataset is not produced through Illumina technologies (DNBseq-BGI). To "test the waters", I ran GRIDSS on a test sample. Although the software runs, the output .vcf file contains only "SVTYPE=BND".
I am wondering whether the vcf output reflects an issue arising from the sequencing output. If so, have you found/could there be a way to adjust the software for non-illumina sequencing output (e.g. through SAMtags etc)? Any help is greatly appreciated :)
Best regards, Domniki