missing insertion

[Danisov]

Hi @brentp I have a question about missing insertion variants. I used sample HG002 for variant calling with smoove using the command below. But it seems strange to me that I can't find the variants of Insertions? Do you have any idea why? does it have a notation instead of INS? Thank you in advance for your answer. Note: I also used a WGS of my samples and I still haven't found the Insertions.

$ singularity run smoove.sif smoove call \
-x \
--name my_project \
--exclude ${BED} \
--fasta ${hg38} \
-p 1 \
--genotype \
 ${input} 

[brentp]

what does this mean:

I can't find the variants of Insertions

? Do you mean duphold isn't annotating your insertions? Can you show a variant VCF line output from duphold that doesn't show what you expect?

[Danisov]

My apologies I wanted to write this issue in smoove not on duphold. Do you want me to delete it and re-write it in the smoove issues?

[brentp]

Here is fine, I just don't have enough information to help you.

[Danisov]

I just noticed that the insertions generated with smoove or lumpy are in BND format. Thanks @brentp