Sniffles

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Very high proportion 0/1 genotype in DUP, BND and INV

3

Hi, I called the SVs using ~15X ONT reads. I found that the DUP, BND, and INV contained a high proportion of 0/1 genotype, with very few 1/1. Do you...

hui-liu

No variant reads reported with Sniffles2 genotyping

4

Hi, I used Sniffles2 to perform genotyping on some deletions when I noticed that it seems to report all reads as reference even though the variant reads are visible on...

phuazjc

combine-output-filtered not working?

1

### Description I am trying to detect somatic structural variants. These variants are supported by few reads in few samples. Therefore, I want to disable quality control and filtering. I...

Will-Tyler

Issues with Sniffles2 for α-Globin SV Detection

2

I have tested Sniffles2 to detect α-globin deletions in long-read sequencing data but encountered several issues that I would like to share. I would appreciate any feedback or suggestions from...

virginied33

Extra filtration after obtaining the VCF / recommended visualize tool for sniffle output

3

Hi everyone, I have been working on human WGS data which is sequenced with ONT. When I run the Sniffles with this command: `sniffles -i input.bam --vcf output.vcf --threads 32`...

enes-ak

Error in download

2

After downloading the all the dependancies I got the following error with conda install -c bioconda sniffles=2.6.1. Could you advise a work around to solve this. The following package could...

sybah2

Expectations regarding discrepancies in individual vs population called VCFs

4

Hi guys!

I hope you could help with a small question regarding Sniffles2 population calling mode, and what we should expect to see (or not!) in multi-sample VCFs vs what...

stallmanGEL

When running Sniffles2, I noticed that BND structural variant calls are being reported with 0-based coordinates instead of the expected 1-based VCF standard. For example: ``` chr21 24015867 Sniffles2.BND.4M26D N...

zaka-edd

Potential missing calls when using ngmlr for alignment

1

Hi, This might not be a big problem but I just wanted to check a patch to an error in NGMLR might cause issues in Sniffles. I'm using NGMLR for...

jamesdgalbraith

Can >3M deletions be detected by sniffles?

1

Hi, Thank you for a great tool! I have two patient samples, both of them have a deletion longer than 3M in chrY, and can be clearly visualized in IGV...

yue131