false genotyping large deletion

[DHmeduni]

Hi, I have a 62kb deletion that is very obviously heterzygous but sniffles is calling it as homozygous even the coverage field its's obvious its heterozygous..... anybody have an idea what to do, or is this a bug?

chr7 148238576 Sniffles2.DEL.4A5S6 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=-62659;END=148301235;SUPPORT=83;COVERAGE=154,75,57,79,157;STRAND=+-;AF=1.000;STDEV_LEN=0.000;STDEV_POS=0.000 GT:GQ:DR:DV 1/1:60:0:83

[mletexier-cnrgh]

Hi @DHmeduni & @fritzsedlazeck ,
I have the same phenomenon, which is repeated on several events, for example, a 39 Kb deletion, which is seen with the 1/1 genotype with sniffles (VAF=100%, (0, 25)) whereas visually in IGV, it is 0/1. Sequences in IGV are sorted according to haplotypes.
I've attached the IGV screenshot.
The parameters used are:
--minsupport 5
--tandem-repeats hs38me.trf.bed
--minsvlen 50
--min-alignment-length 2000
--mapq 20

Thanks for any help you can give
Mélanie

[fritzsedlazeck]

Thanks we can reproduce this now also here.. @lfpaulin is working on that. Hope we have a fix on the next verison.

We found the issue , which is basically handeling the read counting wrong for large split read events.. which is a bug in the deletions but works on all other SV events. In short we are by far undercounting the ref supporting reads , which leads to a 1/1 GT.

Thanks
Fritz

[mletexier-cnrgh]

Thank you very much for your prompt feedback, Fritz.
Looking forward to the next version :)

Mélanie

[tuannguyen8390]

Hi @fritzsedlazeck! Do you have any estimate for when the next release might be coming? We're really looking forward to seeing this fix as this having an impact on our recessive lethal tracking 🍄

[fritzsedlazeck]

We have a working prototype that goes through testing right now. It looks like we resolved it. We hope that we can roll out that new version next week.
Thanks
Fritz

[tuannguyen8390]

Thanks Fritz, really looking forward to it :)

Tuan

[tuannguyen8390]

Sorry for having a back-to-back message Fritz, but would the bug cause error in the existing snf files or can we just run the merge SNF with the new Sniffles version ?

[fritzsedlazeck]

So this is still something we are investigating. @lfpaulin can maybe expand a bit more... the SNF file holds all variants but they have set filters.. These filters can be overwritten with new behavior during the merge, which also applies the same filters.

[lfpaulin]

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 that feature. Theoretically, if the coverage support values are correct in the SNF then they should provide the correct GT, otherwise you may need to re-run them. We have one test case I will check tomorrow, and will let you know our findings

[tuannguyen8390]

Thanks for the input @fritzsedlazeck & @lfpaulin. The files that we received from partners are from v2.2 so it poses some concern our end. We have a few known recessive SV that are not supposed to be 1/1 so it's a relatively straightforward test our end.

[tuannguyen8390]

We test out v.2.5 today. Seems like we need to re-generate the old snf file

1. call from bam

zgrep 91857666 4780_2.5.2.vcf.gz                                                                              

9       91857666        Sniffles2.DEL.E0CS8     N       <DEL>   60      PASS    PRECISE;SVTYPE=DEL;SVLEN=-138347;END=91996012;SUPPORT=15;COVERAGE=34,20,11,13,27;STRAND=+-;STDEV_LEN=0.000;STDEV_POS=0.000;VAF=0.500        GT:GQ:DR:DV     0/1:60:15:15

2. call from 2.5 snf

zgrep 91857666 4780_snf_2.5.2_new_snf.vcf.gz                                                                      
9       91857666        Sniffles2.DEL.2210M8    N       <DEL>   60      PASS    PRECISE;SVTYPE=DEL;SVLEN=-138347;END=91996012;SUPPORT=15;COVERAGE=34,20,11,13,27;STRAND=+-;STDEV_LEN=0.000;STDEV_POS=0.000;VAF=0.500        GT:GQ:DR:DV:ID  0/1:60:15:15:Sniffles2.DEL.E0CS8

3. call from 2.2 snf

zgrep 91857666 4780_snf_2.5.2.vcf.gz

9       91857666        Sniffles2.DEL.2210M8    N       <DEL>   60      PASS    PRECISE;SVTYPE=DEL;SVLEN=-138347;END=91996012;SUPPORT=15;COVERAGE=34,20,11,13,27;STRAND=+-;AF=1.000;STDEV_LEN=0.000;STDEV_POS=0.000 GT:GQ:DR:DV:ID  1/1:41:0:15:Sniffles2.DEL.E0CS8

[fritzsedlazeck]

Sorry for that. I can cross check with the team if there is a mode to rescue form the SNF file.. the SV should be in there but has already a failed tag assigned. @lfpaulin knows this better than I by now ..
Thanks
Fritz

[tuannguyen8390]

Thanks @fritzsedlazeck , would be v. nice if we can have that option. Asking 17 partners to remake their snf is a bit of a nightmare to me 😆.

[fritzsedlazeck]

Yeah... I also have a similar situation. Meeting with @hermannromanek next monday and will discuss. Stay tune pls.
Fritz