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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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Warning: Sample has a non-default paired-end layout! #306

Open liujiaxin7 opened 1 year ago

liujiaxin7 commented 1 year ago

I run delly as follows: delly_v1.1.5_linux_x86_64bit call -g GCF_000001735.4_TAIR10.1_genomic.fna SRR21814509.sorted.marked.bam > delly.vcf

but I encountered a warning!

Warning: Sample has a non-default paired-end layout! The expected paired-end orientation is ---Read1---> <---Read2--- which is the default illumina paired-end layout.

I don't quite understand what this means. Do you have such problems ? How did you deal with it? Thank you in advance！

tobiasrausch commented 1 year ago

This warning usually points to a problem in the library prep.

liujiaxin7 commented 1 year ago

This warning usually points to a problem in the library prep.

Thank you very much. I'm going to check this！

graceooh commented 1 year ago

@tobiasrausch I have the same error and after I ran Alfred it looks like a lot of my samples have the wrong read orientation. Is the only solution to this preparing new libraries? What are some further quality control checks that I can do and is there a way to fix this computationally? Thank you!

tobiasrausch commented 1 year ago

You need to contact the sequencing provider how they prepared the libraries. This doesn't seem like a standard protocol for whole genome sequencing when many of your samples have an unexpected Illumina paired-end layout.

graceooh commented 1 year ago

You need to contact the sequencing provider how they prepared the libraries. This doesn't seem like a standard protocol for whole genome sequencing when many of your samples have an unexpected Illumina paired-end layout.

@tobiasrausch Thank you for your answer! What are some downstream effects of this in variant calling in and outside of SV calling?

tobiasrausch commented 1 year ago

Difficult to say, paired-end mapping will certainly not work.