About the INS sequence in vcf output

[ClarenceHsiang]

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]

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]

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]

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]

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