I am trying to use annotate function of snpsift.
I have downloaded the software using conda.
when i write the command
this is the output:
SnpSift version 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: java -jar SnpSift.jar [command] params... Command is one of: alleleMat : Create an allele matrix output. annotate : Annotate 'ID' from a database (e.g. dbSnp). Assumes entries are sorted. caseControl : Compare how many variants are in 'case' and in 'control' groups; calculate p-values. ccs : Case control summary. Case and control summaries by region, allele frequency and variant's functional effect. concordance : Concordance metrics between two VCF files. covMat : Create an covariance matrix output (allele matrix as input). dbnsfp : Annotate with multiple entries from dbNSFP. extractFields : Extract fields from VCF file into tab separated format. filter : Filter using arbitrary expressions geneSets : Annotate using MSigDb gene sets (MSigDb includes: GO, KEGG, Reactome, BioCarta, etc.) gt : Add Genotype to INFO fields and remove genotype fields when possible. gtfilter : Filter genotype using arbitrary expressions. gwasCat : Annotate using GWAS catalog hwe : Calculate Hardy-Weimberg parameters and perform a godness of fit test. intersect : Intersect intervals (genomic regions). intervals : Keep variants that intersect with intervals. intIdx : Keep variants that intersect with intervals. Index-based method: Used for large VCF file and a few intervals to retrieve join : Join files by genomic region. op : Annotate using an operator. phastCons : Annotate using conservation scores (phastCons). private : Annotate if a variant is private to a family or group. rmRefGen : Remove reference genotypes. rmInfo : Remove INFO fields. sort : Sort VCF file/s (if multiple input VCFs, merge and sort). split : Split VCF by chromosome. tstv : Calculate transiton to transversion ratio. varType : Annotate variant type (SNP,MNP,INS,DEL or MIXED). vcfCheck : Check that VCF file is well formed. vcf2tped : Convert VCF to TPED. Options common to all SnpSift commands: -d : Debug. -download : Download database, if not available locally. Default: true. -noDownload : Do not download a database, if not available locally. -noLog : Do not report usage statistics to server. -h : Help. -v : Verbose.
But once i try and write the command to annotate my .vcf files with rsid in dbSNP its showing error: the code:
java -jar SnpSift.jar 00-All.vcf GEUVADIS.chr2.genotype.vcf > variants_annotated.vcf the error: Error: Unable to access jarfile SnpSift.jar