VariantAnnotator GATK Error
I' m trying to get rs ID# in my .vcf file which i have generated through samtools. I am using GATK VariantAnnotator to get rs ID# in my vcf file.
java -jar GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -R ambda_virus.fa -T VariantAnnotator -I local_sorted.bam -o output.vcf --variant sim_variants.vcf -L sim_variants.vcf --dbsnp 00-All.vcf
but getting this error:
ERROR MESSAGE: Fasta index file /home/bio1/Desktop/Shivangi/BOWTIE/bowtie2-2.2.3/example/reference/lambda_virus.fa.fai.fai for reference /home/bio1/Desktop/Shivangi/BOWTIE/bowtie2-2.2.3/example/reference/lambda_virus.fa.fai does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.
please let me know, these command line arguments are okay?
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Firstly, the command you posted wouldn't create that error message (you have a typo). Secondly, I suspect that you used
-R lambda_virus.fa.fairather than-R lambda_virus.fa, since that would indeed cause that error. Try running the command again like that and see if the error still occurs (if so, just copy and paste the exact command you used into a new comment).