error related to SnpSift
Entering edit mode
8 weeks ago
rheab1230 ▴ 20

hello everyone, I am trying to use annotate function of snpsift. I have downloaded the software using conda. when i write the command SnpSift 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
rsid SnpSift SNP • 166 views
Entering edit mode
8 weeks ago
rheab1230 ▴ 20

I am able to do this. I downloaded the .tar file instead of using conda


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