Luis Paulin comments

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                                            Luis Paulin

false genotyping large deletion

The SNF file is "primed" with a filter, however during the merge it can be override if there is support in other samples. Regarding the genotype we are still testing...

Invalid END position

@hermannromanek it looks like Sniffles is diminishing by 1 the end when outputting the END position and for INS its the same as start that when is **1** it becomes...

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

Dear Enes, For single sample calling, the number of threads should be at most the number of chromosomes in the reference genome that was used for alignment as Sniffles will...

using SNV/SNP file with spectre in tumour samples

Hi @eesiribloom > I assume it is preferred to input SNPs from a matched tumour sample rather than germline SNPs? Or would germline SNPs be more informative as these are...

<INS> sequence missing in ALT field and represented as C<INS>, T<INS>, A<INS>, G<INS>

Thanks @leone93 for the examples. It looks like when we are missing the INS sequences (symbolic) then the `` is added to the ALT column, moreover, then we are adding...

Can >3M deletions be detected by sniffles?

Hi @yue131 Can you share with us which version of Sniffles are you using and can you share any BAM files

sniffles 2.5 produces variant longer than contig

@hermannromanek check if POS and END are 0-based or 1-based we had had discussion some months ago with a file having a POS=0

Type of BND connection mislabeled

Hi Ryan not yet, we are currently in the testing phase of the new release (1-4 weeks) and this fix might be included there

Executing the command `sniffles -i reads_region.bam -v test.vcf --tandem-repeats human_hs37d5.trf.bed --reference genome_mfa.CT_conversion.fa` results in the following error: Segmentation fault (core dumped)

Hi @lillianokok can you try running sniffles v2.6.3 please Best Luis

Executing the command `sniffles -i reads_region.bam -v test.vcf --tandem-repeats human_hs37d5.trf.bed --reference genome_mfa.CT_conversion.fa` results in the following error: Segmentation fault (core dumped)

Hi @lillianokok have you tried any other version? we just released [v.2.7.0](https://github.com/fritzsedlazeck/Sniffles/releases/tag/v2.7.0), also how do you install sniffles (pip, conda, docker/singularity)