search

dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
413 stars 136 forks source link

About the INS sequence in vcf output #344

Open ClarenceHsiang opened 10 months ago

ClarenceHsiang commented 10 months ago

image Dear Delly team,

Good evening. In the output vcf file, Alt showed without the insertion sequence, is the INS sequence in the INFO column?

Thanks again

tobiasrausch commented 10 months ago

This seems to be a VCF file after snpEff processing. Can you please check the original output VCF of delly if the ALT column contains symbolic values like or the inserted nucleotide sequence?

ClarenceHsiang commented 10 months ago

image

Hello, I checked the original vcf, BND showed this kind of information (i.e. ]Pmu3_1:7879959]T) in ALT column, for other SVs (DEL, INS .. ) are the same to the previous file.

I did the process of variant calling as below, By followering Germline SV calling, I converted the germline.bcf to vcf through bcftools view function. Then, the output vcf showed as the attached figure.

tobiasrausch commented 10 months ago

I see. Thanks for letting me know. I will try to fix this in the next version, for an insertion there should always be an ALT sequence. For the time being, you can then only use INFO/CONSENSUS which indeed includes the inserted sequence but also surrounding sequence.

ClarenceHsiang commented 10 months ago

Thank you so much. Is there any way that we can extract the insertion sequence?