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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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why there's SV that all samples showing reference allele #358

Open shuiyanwu778 opened 3 years ago

shuiyanwu778 commented 3 years ago

Hey, Please see my attached files, after I conducted "lumpyexpress -B $(echo $(ls -d gz.bam)|sed 's/ /,/g') -S $(echo $(ls -d ters.bam)|sed 's/ /,/g') -D $(echo $(ls -d *ants.bam)|sed 's/ /,/g') -x exmerge.bed -o 349all.vcf", I found that some variants in the list have no alleternative allele. So whether it's due to my bad operation or it's just the program bug. If so, whether there's necessary steps for SVs called by lumpy? such as filter false variants, etc.?

Thanks, Cyan sv_ref.txt

ryanlayer commented 3 years ago

If you are referring to the N in the ALT field, we do that instead of putting the sequence. If you are referring to the fact that all of your genotypes are "0/0", that is because we run svtyper to genotype and in some cases all of the genotypes come back as reference. This is expected.

On Thu, Apr 22, 2021 at 8:47 PM shuiyanwu778 @.***> wrote:

Hey, Please see my attached files, after I conducted "lumpyexpress -B $(echo $(ls -d gz.bam)|sed 's/ /,/g') -S $(echo $(ls -d ters.bam)|sed 's/ /,/g') -D $(echo $(ls -d *ants.bam)|sed 's/ /,/g') -x exmerge.bed -o 349all.vcf", I found that some variants in the list have no alleternative allele. So whether it's due to my bad operation or it's just the program bug. If so, whether there's necessary steps for SVs called by lumpy? such as filter false variants, etc.?

Thanks, Cyan sv_ref.txt https://github.com/arq5x/lumpy-sv/files/6362351/sv_ref.txt

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shuiyanwu778 commented 3 years ago

Thank you for the reply. I'm just wondering why locus with genotypes are "0/0" is called as a SV? So I must filter these sites manually before downstream analysis.

ryanlayer commented 3 years ago

It was a false positive that was corrected by svtyper and yes, filter by allele count.

On Apr 24, 2021, at 9:11 PM, shuiyanwu778 @.***> wrote:

 Thank you for the reply. I'm just wondering why locus with genotypes are "0/0" is called as a SV? So I must filter these sites manually before downstream analysis.

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changhan1110 commented 1 year ago

If you are referring to the N in the ALT field, we do that instead of putting the sequence.

Why do you do that? What is the reason?

ryanlayer commented 1 year ago

Many of the SVs are very large. Including the deleted sequences in the ALT field would make manual inspecting the VCF very difficult.

On Mon, Aug 28, 2023 at 11:37 PM James Hashfield @.***> wrote:

If you are referring to the N in the ALT field, we do that instead of putting the sequence.

Why do you do that? What is the reason?

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