Hi there, We met a syntax error when we using VEP with dbNSFP.pm to annotate variants.
perl /home/zoeching/Tools/src/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl\
--offline \
--fork 10\
--pick\
--merged /home/zoeching/pku/Ref\
--everything \
--force_overwrite\
--vcf \
--vcf_info_field CSQ\
--plugin dbNSFP,/home/zoeching/pku/Ref/dbNSFPv2.9.1/dbNSFP.gz,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,CADD_raw,CADD_raw_rankscore,CADD_phred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore\
--plugin LoF,human_ancestor_fa:/home/zoeching/pku/Ref/human_ancestor.fa.gz\
-i /work1/ASD/Data/other/ASD569_1.gatk-queue_raw_snps.vcf \
-o ASD569_1.gatk-queue_raw_ann_snps.vcf
after ran the command, I got this:
The output (if any) follows:
2016-09-04 16:02:10 - Read existing cache info 2016-09-04 16:02:10 - INFO: Disabling --hgvs; using --offline and no FASTA file found 2016-09-04 16:02:10 - Failed to compile plugin dbNSFP: syntax error at /home/zoeching/Tools/library/perl_module/lib/perl5/dbNSFP.pm line 304, near "s/[|]/&/gr" Compilation failed in require at (eval 68) line 2. BEGIN failed--compilation aborted at (eval 68) line 2.
2016-09-04 16:02:11 - Loaded plugin: LoF 2016-09-04 16:02:11 - Starting... 2016-09-04 16:02:11 - Detected format of input file as vcf 2016-09-04 16:02:11 - Read 5000 variants into buffer 2016-09-04 16:02:11 - Calculating consequences
and this
Bareword found where operator expected at /home/zoeching/Tools/library/perl_module/lib/perl5/dbNSFP.pm line 304, near "s/[|]/&/gr" i didn't get the mean of "r" in "s/[|]/&/gr",line304
so i deleted "r" and ran the command again. At this time, no errors came out but the annotation failed. The columns for annotation from dbNSFP.gz were empty. And i can successfully use "chr pos" to grep infomation from dbNSFP2.9.1_variant.chr* file. So, the input file is okay.
Anyone met this error before? Anything wrong with dbNSFP.pm(line 304)? What does the "r" means here?
OK. Thx for your help.