i was working on Variant Annotation ...the error was genes.gff not found

[singha30]

Command executed:

bcftools annotate --header-lines /Data/data/raja/cfdna/nextflow1/bin/syn3_header.txt LCR_FILTERED > FILTERED_hd.vcf java -jar -Xmx4g /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.jar eff -dataDir /Data/data/raja/cfdna/nextflow1/bin /snpEff/data -cancer -noLog -csvStats CSV_STATS -s HTML_REPORT /Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14 FILTERED_hd.vcf > SNPEFF_ANNOTATED.vcf java -jar /Data/data/raja/cfdna/nextflow1/bin/SNPEFF/SnpSift.jar annotate /Data/data/raja/cfdna/nextflow1/bin/snpEff/DBS NP_DATABASE -tabix -noLog SNPEFF_ANNOTATED.vcf > DBSNP_ANNOTATED.vcf

Command exit status: 255

Command output: (empty)

### Command error: java.lang.RuntimeException: Property: '/Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14.genome' not found at org.snpeff.interval.Genome.(Genome.java:103) at org.snpeff.snpEffect.Config.readConfig(Config.java:757) at org.snpeff.snpEffect.Config.init(Config.java:532) at org.snpeff.snpEffect.Config.(Config.java:119) at org.snpeff.SnpEff.loadConfig(SnpEff.java:449) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:883) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:869) at org.snpeff.SnpEff.run(SnpEff.java:1173) at org.snpeff.SnpEff.main(SnpEff.java:163)

1. link Variant Annotation using snpEff :- https://github.com/hbctraining/variant_analysis/blob/main/lessons/11_variant_annotation.md
2. code :- **# Run SnpEff java -jar -Xmx4g $SNPEFF/snpEff.jar eff \ -dataDir $DATADIR \ -cancer \ -noLog \ -csvStats $CSV_STATS \ -s $HTML_REPORT \ $REFERENCE_DATABASE \ $FILTERED_VCF_FILE_WITH_PEDIGREE_HEADER \

   $SNPEFF_ANNOTATED_VCF_FILE**

Let's breakdown this command and discuss each argument:

• java -jar $SNPEFF/snpEff.jar eff Snpeff This calls the eff package within SnpEff to annotate variants.
• -dataDir $DATADIR This is the path to the data directory that holds the SnpEff annotations
• -cancer Performs cancer-mode
• -noLog This does not report command usage to SnpEff's server
• -csvStats $CSV_STATS This produces a flat-text file with summary statistics regarding the variants annotated. (Optional)
• -s $HTML_REPORT This creates an HTML file with summary statistics regarding the variants annotated. This HTML file is mostly just an HTML stylized version of the CSV file above. (Optional)
• $REFERENCE_DATABASE This is the SnpEff database we are going to use for the annotation.
• $FILTERED_VCF_FILE_WITH_PEDIGREE_HEADER This is the input VCF file to be annotated

• $SNPEFF_ANNOTATED_VCF_FILE The output of SnpEff will be redirected into this VCF file.

[singha30]

1.This is the code which i was trying to run :- **java -jar -Xmx4g /Data/data/raja/cfdna/nextflow1/bin/snpEff/snpEff.jar eff -dataDir /Data/data/raja/cfdna/nextflow1/bin/snpEff/data -cancer -noLog -csvStats CSV_STATS -s HTML_REPORT /Data/data/raja/cfdna/nextflow1/bin/snpEff/Data/data/GRCh38.p14 FILTERED_hd.vcf > SNPEFF_ANNOTATED.vcf

2. I was working on the Gatk Variant Annotation
3. i have followed the step of snpEff

[PriyaV229]

hello @singha30 I think you have missed out some step so this error is showing up

1. you had loaded the SnpEff module
2. download REFERENCE DATABASE as given in the doc
3. Setting up Cancer-mode using the txt file and sbatch

   Using SnpEff to annotate our variants

   Load modules

   Assign variables

   etc....... then Submit this script using: sbatch variant_annotation_normal_tumor.sbatch Tip: Next time maybe you can attach log files instead of copy pasting the content.