8000 End position occurs before start position · Issue #31 · friend1ws/nanomonsv · GitHub
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End position occurs before start position #31

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zhemingfan opened this issue Feb 23, 2023 · 4 comments
Open

End position occurs before start position #31

zhemingfan opened this issue Feb 23, 2023 · 4 comments

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@zhemingfan
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zhemingfan commented Feb 23, 2023 •
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Hi @friend1ws ,

I've noticed that in the final output we received a call similar to:
chr6    31427745        d_1188  A       <INS>   .       Too_small_size  END=31427708;SVTYPE=INS;SVINSLEN=0;SVINSSEQ=    TR:VR   107:8   61:0
Is there a possibility to add a check to coerce the end positions to be equal or greater than the start position for insertions and deletions?

Thanks
@zhemingfan zhemingfan changed the title Runtime wrong. End position occurs before start position Feb 23, 2023
@kojix2
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kojix2 commented Apr 29, 2023

Thank you for sharing your experience.

I encountered the same issue where the Circos Plot could not be displayed in the SV inspector of jbrowser2 due to the following record:

chr7	61067874	d_338	T	<INS>	.	Too_small_size	END=61067865;SVTYPE=INS;SVINSLEN=14;SVINSSEQ=TGAATCAAATGGTG	TR:VR	60:16	23:0

As shown in the screenshot below:

image

When I ran bcftools view tumor.nanomonsv.result.vcf, I received the following warning message:

[W::vcf_parse_info] INFO/END=61067865 is smaller than POS at chr7:61067874

@friend1ws
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8000
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Thank you very much.
These variants should be filtered due to the Too_small_size tags.
However, I would like to develop a more general solution.
These might be categorized as DUP or DUP:TANDEM instead of INS.

@RenzoTale88
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@friend1ws I've come across this too on a number of sites with v0.7.1. Several of them are not filtered for small size either.

@friend1ws
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OK. will try to solve in the next version.

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@friend1ws @kojix2 @RenzoTale88 @zhemingfan
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