FunMotifs: missing annotation

[robertzeibich]

I tried to annotate my files with FunMotifs, but did not succeed:
Screenshot form the bed file:

Created test VCF - last record in the VCF meets the first record in the BED file:

FunMotifs remains empty:

That is the command I used:
vep -i ${WORKDIR}/input.vcf -e -o ${WORKDIR}/output.vcf --vcf --pick --cache --dir_cache ${HOMO}
--fasta ${FASTA} --fork 2 --offline --merged --assembly GRCh38 --buffer_size 1000
--force_overwrite
--plugin FunMotifs,${BED}/all_tissues.funmotifs_sorted_mapped.reordered.sorted.hg38.reordered.sorted.bed.gz,blood,brain,breast

Any idea why the annotation failed?

I also attached the files for investigation.

VCF: input.vcf.txt

BED FILE: all_tissues.funmotifs_sorted_mapped.reordered.sorted.hg38.reordered.sorted.head.bed.gz

TABIX FILE: all_tissues.funmotifs_sorted_mapped.reordered.sorted.hg38.reordered.sorted.head.bed.gz.tbi.txt

OUTPUT: output.vcf.txt

[olaaustine]

Hi @robertzeibich,
Hope this meets you well?
Thank you for sharing the files and the command used.
I am unable to recreate this issue and using the BED file you shared, there is an issue with the header line which is not allowing it to be tabixed properly.
Please follow the BED format header line format as seen here and tabix it again and run the command again.
Please let us know if this solves the issue.
Thank you so much.
Ola.

[robertzeibich]

Thank you for getting back to me, Ola.

Unfortunately, I am not able to resolve the issue.
When I use the required fields, I get the following error: WARNING: Failed to instantiate plugin FunMotifs: Insufficient input parameters found for FunMotifs plugin.
When I remove the header line and the last column, I still do not get any annotation information.

Where you able to get the annotation running with the files I provided?

Information to my bed file: I did a liftover of the following bedfile: http://bioinf.icm.uu.se:3838/funmotifs/ --> All motifs: fscore per tissue type (.tbi)
I only kept the liftover information in the last column.

[olaaustine]

Hi @robertzeibich,
Hope this meets you well?
Yes, I was able to run the annotation with the file given.
Is this what the header of your BED file looks like
#chrom start end name score strand pval blood brain breast cervix colon esophagus kidney liver lung myeloid pancreas prostate skin stomach uterus hg19
If not, please can you correct the header of your file and let us know if that resolves the issue.
Thank you
Ola.

[robertzeibich]

Did not resolve the issue. Please share the updated input file, the output file and the command you use.

Thank you.
Robert

[olaaustine]

Hi @robertzeibich,
The updated input FunMotifs file just has the header changed as suggested earlier.
I did not make any changes to the input vcf file.
The command applied is the same command above. I am still unable to create your issue
Just to clarify what tabix are you using, can you run "which tabix" and also whats the error message you are getting
Thank you
Ola.

[robertzeibich]

bgzip 1.19
tabix 1.19
VEP/107

I am not getting an error anymore. However, I am still missing the annotation in the third record.

[olaaustine]

Can you try with the latest release (release 112) of VEP and VEP plugins, what do you mean by third record?
Thank you
Ola

[robertzeibich]

Could you please share your annotated output file?

[olaaustine]

Hi @robertzeibich,
Hope you are well?
Please can you try with the latest release of VEP and also what do you mean by third record?
Thank you
Ola