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hbctraining / variant_analysis

https://hbctraining.github.io/variant_analysis/
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hg38.fa.genome #7

Closed singha30 closed 10 months ago

singha30 commented 11 months ago

please let me know how to get this file. for calling the following command 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

Gammerdinger commented 10 months ago

Hi singha30,

These course materials are still under active development, we are hoping to have them completed by early Summer 2024. The short answer is that the $SNPEFF_ANNOTATED_VCF_FILE is the output from MuTect2 after filtering and also after annotation from SNPeff. We hope this helps!

Best, Will Gammerdinger

singha30 commented 9 months ago

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. error is show:-GRCh38.p14.genome' not found can you please help how to generate this file or fix the issue