Help with error in snpEff command
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17 months ago
Chris ▴ 340

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.

snpEff • 2.0k views
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17 months ago
cfos4698 ★ 1.1k

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.

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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]

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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?

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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.

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17 months ago

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?

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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?

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I don't understand your problem/question.

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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.

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I appreciate your help 😃!

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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?

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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.

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