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No sequence reported for DELs with AF=1

See original GitHub issue

Hi Fritz,

I noticed that Sniffles (v1.0.10) does not report sequence for DELs that have an allele frequency of 1 (like in the samplot below), but it does so for all other DELs.

chr2L	1678983	178	N	<DEL>	.	PASS	PRECISE;SVMETHOD=Snifflesv1.0.10;CHR2=chr2L;END=1686432;ZMW=218;STD_quant_start=0.897758;STD_quant_stop=1.165422;Kurtosis_quant_start=49.558380;Kurtosis_quant_stop=65.947128;SVTYPE=DEL;RNAMES=(...);SUPTYPE=SR;SVLEN=-7449;STRANDS=+-;RE=268;REF_strand=0,0;AF=1	GT:DR:DV	1/1:0:268

del

If these seqs represent the reference region that was deleted is there a reason for this behavior?

Thanks, Gui

Issue Analytics

State:
Created 5 years ago
Comments:5 (3 by maintainers)

Top GitHub Comments

1reaction

fritzsedlazeckcommented, Mar 12, 2019

Hi Gui, thanks for reaching out. It might be simple. Sniffles is currently not using the reference sequence. So for deletions, we can give you the sequence for an alignment event but not for a split read event.

I might need to extend this to cover these cases too. I will put an enhance flag on this for the time being.

Thanks Fritz

0reactions

fritzsedlazeckcommented, Feb 8, 2022

We just pushed a completely new version of Sniffles (v2.0.0.2) and hope this will be resolved.