Entering edit mode
3 months ago
melissachua90
▴
70
# 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)
Would you be more specific to your question? Do you mean how to debug this syntax error?
there is no
--allsample
option in the "usage" screen you're showing. I suspect you're using an old version ?