Fully supported CRISPR edit not detected.

[caonetto]

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 supporting the deletion. The variant details are attached. Any idea whats going on???
Thanks.

Chr: contig_15
Position: 388104-388168
ID: Sniffles2.DEL.1B3S13
Reference: GTTGACAGCAACAACCTCAATGTCTTTTCTTTGCAAAGCCAATCTCAAGACCAATCTACCGATT*
Alternate: N
Qual: 60
Type: INDEL
Is Filtered Out: Yes
- STDEV_POS

Alleles:
Alternate Alleles: N
Allele Frequency: 1.0

Variant Attributes
Allele Frequency: 1.000
SUPPORT: 416
COVERAGE: [334, 339, 342, 342, 337]
SVTYPE: DEL
STDEV_POS: 1057.435
END: 388168
SVLEN: -64
![Screenshot from 2023-09-25 17-14-43](https://github.com/fritzsedlazeck/Sniffles/assets/25968988/30d7c30d-7194-424f-a282-abdfbf616e07)

STDEV_LEN: 2.267
IMPRECISE: true
STRAND: +-
NM: 0.043

[caonetto]

Hi @fritzsedlazeck
Just adding to these topic, just discovered another CRISPR homozygous deletion which is not even called at all, does not appear with the --no-qc flag and has very high coverage.

[caonetto]

Strangely, as soon as I remove the --minsupport 10 flag this variant is detected even though there are clearly more than 10 bp supporing it. ?

[fritzsedlazeck]

@lfpaulin is that the issue with too high coverage? I remember that there was something.. right ?