gff format for GRCh38

[redincla]

Good afternoon,

I've been trying desperately to annotate my final vcf file as the last step for smoove, using genome version hg38. However, when I use the gencode gff3 file, I get the following error:

singularity run smoove  annotate --gff gencode.v39.annotation.gff3.gz test.smoove.square.vcf.gz | bgzip -c > test.smoove.square.anno.vcf.gz
WARNING: group: unknown groupid 124638
[smoove] 2022/03/08 15:09:37 starting with version 0.2.7
2022/03/08 15:09:49 no records found with 'gene' type in gff

And when I use the gff file from NCBI, I get the following:

singularity run smoove annotate --gff GCA_000001405.28_GRCh38.p13_genomic.gff.gz test.smoove.square.vcf.gz | bgzip -c > test.smoove.square.anno.vcf.gz
WARNING: group: unknown groupid 124638
[smoove] 2022/03/08 14:54:34 starting with version 0.2.7
2022/03/08 14:54:34 no records found with 'transcript' or 'mRNA' type in gff

I'm guessing the file I'm using is not the one smoove expects as an input (even though the Gencode file does contain gene type entries). Is smoove not accepting gff3 formats? Or any idea why I get this error? Alternatively, where can I download the appropriate gff/gff3 file for GRCH38/hg38?

Thanks a ton,

Claire

[brentp]

Hi Claire, did you try the gff from here: http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/

? that should show when you run smoove annotate without any arguments.

[redincla]

Thanks for the heads up! I had tried to run annotate without the -gff argument for help but still providing the vcf input so it didn't show anything but an empty file error. So with the Ensembl gff3 file it sorts of work, but the annotation somehow get stalled in the way and it stops annotating after a few entries, so the output file is truncated compared to the unannotated vcf. I'll try to see if I can find the reason.

Claire

On Tue, Mar 8, 2022 at 3:30 PM Brent Pedersen @.***> wrote:

Hi Claire, did you try the gff from here: http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/

? that should show when you run smoove annotate without any arguments.

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[brentp]

Someone else just reported something similar here: https://github.com/brentp/smoove/issues/188 if you can get me a way to recreate this problem I can look into it. It could be something with the gff format changing, so you could also try an older ensembl release.

And another thing to try is to use svpack consequence instead.