Sniffles

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1

anduin0909

reference letter case issue in VCF

1

HI, sniffles2 VCF results contain sequences in lower case while the reference genome is higher case in that location. This leads to crashing when I phase the VCF using hiphase...

splaisan

Fully supported CRISPR edit not detected.

5

Hi, I have a known homozygous deletion made using CRISPR which is not getting detected by sniffles 2.2 due to "STDEV_POS" The sample is super high coverage with 416 reads...

caonetto

--sample-id does not work in force calling mode

3

Output VCF from force calling ignores "--sample-id " parameter and just takes sample ID of the VCF used as input. Command used: $sniffles --input hg004.bam --sample-id HG004_regt --genotype-vcf input.vcf.gz --vcf...

biorococo

When finding leads from split primary alignments, a mapq filter is applied (read_itersplits method) https://github.com/fritzsedlazeck/Sniffles/blob/595a27a55f7d2619c6bdd647de694e737f290315/src/sniffles/leadprov.py#L449 The same filter is commented out for supplementary alignments (see read_itersplits_bnd method). https://github.com/fritzsedlazeck/Sniffles/blob/595a27a55f7d2619c6bdd647de694e737f290315/src/sniffles/leadprov.py#L285 Does this...

HillJamie

I have a sniffles vcf for a plant genome. I am trying to plot the bnd variants as ribbons in circos. Sniffles doesn't provide the end positions for bnd variants....

deepti100rao

How to specify pedigree information in multisample calling mode?

2

How do we specify pedigree information for families or trios for multisample calling mode?

tnguyengel

-b, --bed to call variants only in the provided bed regions

4

For smooth performant integration of Sniffles2 in existing workflows it would be great if a `-b, --bed call variants only in the provided bed regions` command-line argument would exist similar...

dennishendriksen

Hello, Thank you for developing the software! I use Sniffles 2.0.7 in default mode to detect SVs sequenced from a control and an edited sample. In the edited sample, there...

ErminZ

Always using `N` for `REF` in VCF output doesn't seem to be allowed by the VCF spec, and breaks `vg`

4

On the vg project, we've had people report that they are having trouble using VCFs from Sniffles2 with our `vg` tool. Sniffles2 appears to always use `N` for the `REF`...

adamnovak