use snpEff to annotate vcf file

[sytiger]

Dear all,

I am a green-hand for SNP analysis. I use GATK generate the vcf file for staph aureus. Now I need to add annotation to it.

I tried snpEff, how every I get errors

java -Xmx4g -jar snpEff.jar eff -v -c snpEff.config NC_003923.1 snp.filtered.vcf >test.vcf


00:00:00.000 Reading configuration file 'snpEff.config'. Genome: 'NC_003923.1'
00:00:00.517 done
00:00:00.517 Reading database for genome version 'NC_003923.1' from file 'snpEff/./data/NC_003923.1/snpEffectPredictor.bin' (this might take a while)
00:00:01.149 done
00:00:01.162 Building interval forest
00:00:01.627 done.
00:00:01.627 Genome stats :
# Genome name : 'Staphylococcus aureus'
# Genome version : 'NC_003923.1'
# Has protein coding info : true
# Genes : 2704
# Protein coding genes : 2624
# Transcripts : 2624
# Avg. transcripts per gene : 0.97
# Protein coding transcripts : 2624
# Length errors : 0 ( 0.00% )
# STOP codons in CDS errors : 0 ( 0.00% )
# START codon errors : 193 ( 7.36% )
# STOP codon warnings : 0 ( 0.00% )
# Total Errors : 193 ( 7.36% )
# Cds : 2624
# Exons : 2624
# Exons with sequence : 2624
# Exons without sequence : 0
# Avg. exons per transcript : 1.00
# Number of chromosomes : 1
# Chromosomes names [sizes] :
# 'NC_003923' [2820462]

00:00:02.167 Predicting variants

ERRORS: Some errors were detected
Error type Number of errors
ERROR_CHROMOSOME_NOT_FOUND 21718


00:00:04.685 Creating summary file: snpEff_summary.html
log4j:WARN No appenders could be found for logger (freemarker.cache).
log4j:WARN Please initialize the log4j system properly.
00:00:05.151 Creating genes file: snpEff_genes.txt
00:00:05.289 done.
00:00:05.291 Logging
00:00:06.295 Checking for updates...
The output looks like this

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MED1951
gi|21281729|ref|NC_003923.1| 1194 . C T 7492.0 PASS AC=1;AF=1.00;AN=1;DP=245;DS;Dels=0.00;FS=0.000;HaplotypeScore=6.1191;MLEAC=1;MLEAF=1.00;MQ=51.36;MQ0=1;QD=30.58;EFF=NONE(MODIFIER||||||||||1|ERROR_CHROMOSOME_NOT_FOUND) GT:ADP:GQ:MLPSAC:MLPSAF:PL 1:0,240:245:99:1:1.00:7522,0


Thanks