Help with error in snpEff command

Question

[Chris]

Hi all, I do variant annotation using:

snpEff eff variants2_unzip.vcf > output_ann.vcf

java.lang.RuntimeException: Property: ‘variants2_unzip.vcf.genome’ not found.

I read snpeff -h and tried some options and still got the same error.

Would you please have a suggestion? Thank you so much.

snpEff eff hg19 variants2_unzip.vcf > output_ann.vcf doesn't have error but the ID column still missing with only dot and seems there is no difference with the original vcf file.

Answer 1

[cfos4698]

From the program:

Usage: snpEff [eff] [options] genome_version [input_file]

With your command, you don't specify a genome database for the annotation:

snpEff eff variants2_unzip.vcf > output_ann.vcf

That's why your first command fails with an error.

Make sure you specify a reference genome database that matched your organism. Try: snpEff databases.

[Chris]

Thank you! I tried hg19 as the command above but the ID columns still missing with only dot.

snpEff databases

Genome Organism Status Bundle
Database download link

---

129S1_SvImJ_v1.86 Mus_musculus_129s1svimj
http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_129S1_SvImJ_v1.86.zip AKR_J_v1.86 Mus_musculus_akrj
http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_AKR_J_v1.86.zip A_J_v1.86 Mus_musculus_aj

snpeff -h

SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
Usage: snpEff [command] [options] [files]

[cfos4698]

What is your organism that you want to annotate against? You should have seen a big output from snpEff databases. Was it there? Is it hg19 or was that just a trial of any organism? Are you getting any annotations in the INFO column of the VCF?

[Chris]

It is human. Yes, big output so I only took the first two. I see some differences after annotation but didn't as I expected because I don't see the ID value.

Answer 2

[Pierre Lindenbaum]

doesn't have error but the ID column still missing with only dot and seems there is no difference with the original vcf file.

How to add rsIDs to VCF?

[Chris]

Thank you so much for the link!

bcftools annotate -a /data/references/hg19/pipe/dbsnp138/00-All.vcf.gz -c ID -o samtools_annotated.vcf.gz samtools.vcf.gz

After reading this: https://samtools.github.io/bcftools/howtos/annotate.html I am not sure my equivalent file for 00-All.vcf.gz in the command above. Would you please have a suggestion?

[Pierre Lindenbaum]

I don't understand your problem/question.

[Chris]

I mean I need an equivalent file with 00-All.vcf.gz. A file that need to use for annotation but I don't know where to get this file.

[Pierre Lindenbaum]

https://ftp.ncbi.nih.gov/snp/pre_build152/organisms/human_9606_b150_GRCh37p13/VCF/00-All.vcf.gz

[Chris]

I appreciate your help 😃!

[Chris]

This file is pretty big (7 Gb) so I try:

wget https://ftp.ncbi.nih.gov/snp/pre_build152/organisms/human_9606_b150_GRCh37p13/VCF/00-All.vcf.gz

But it didn't work. Would you please have a suggestion?

[Pierre Lindenbaum]

But it didn't work

[Chris]

I am sorry! Mean after I hit enter, nothing happened, so I decided to download it on my computer manually and then upload it to the server.