How to generate table_annovar from VCF input?
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Entering edit mode
5 weeks ago
# Convert VCF to ANNOVAR input format
convert2annovar.pl --format vcf4 --allsample --outfile $ANNOVAR_OUTPUT_DIR/vcf.avinput $VCF_FILE

# Annotate using ANNOVAR
table_annovar.pl $ANNOVAR_OUTPUT_DIR/vcf.avinput $ANNOVAR_DB_DIR \
    -buildver hg38 \
    -out $ANNOVAR_OUTPUT_DIR/cohort \
    -remove \
    -protocol refGene,ensGene,knownGene,clinvar_20210501,cosmic70,dbnsfp35a,gnomad211_exome,gnomad30_genome,intervar_20180118,avsnp150,dbscsnv11,dbnsfp30a,dbnsfp31a_interpro,dbnsfp33a,dbnsfp35c \
    -operation g,g,g,f,f,f,f,f,f,f,f,f,f,f,f \
    -nastring . \
    -vcfinput
    -Otherinfo

Traceback:

Syntax error
Usage:
     convert2annovar.pl [arguments] <variantfile>
     Optional arguments:
            -h, --help                      print help message
            -m, --man                       print complete documentation
            -v, --verbose                   use verbose output
                --format <string>           input format (default: pileup)
                --includeinfo               include supporting information in output
                --outfile <file>            output file name (default: STDOUT)
                --snpqual <float>           quality score threshold in pileup file (default: 20)
                --snppvalue <float>         SNP P-value threshold in GFF3-SOLiD file (default: 1)
vcf annovar • 327 views
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Entering edit mode

Would you be more specific to your question? Do you mean how to debug this syntax error?

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Entering edit mode

there is no --allsample option in the "usage" screen you're showing. I suspect you're using an old version ?

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