NOTICE: output files will be written to .<samplename>.avinput， cannot write to outfile

[sakhdbx]

when i use convert2annovar.pl to transform a vcf file, which includes many samples,so i used '-allsample'.Then,there is a bug:
the code i use:
#perl ~/biosoftware/annovar/convert2annovar.pl -format vcf4 test.vcf -outfile test_annovar -allsample
bug:
#NOTICE: output files will be written to test_annovar..avinput
#cannot write to outfile

So,anyone can tell me how to address the problem,
thanks!

[kaichop]

In general do not use convert2annovar unless there is a special reason to do so. If you want to annotate a file, just use table_annovar with -vcfinput argument. If a file cannot be written usually it will give a reason, so you need to copy and paste the entire message after you run the program exactly as shown in your terminal.

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On Tue, May 10, 2022 at 7:32 AM sakhdbx ***@***.***> wrote: when i use convert2annovar.pl to transform a vcf file, which includes many samples,so i used '-allsample'.Then,there is a bug: the code i use: #perl ~/biosoftware/annovar/convert2annovar.pl -format vcf4 test.vcf -outfile test_annovar -allsample bug: #NOTICE: output files will be written to test_annovar..avinput #cannot write to outfile So,anyone can tell me how to address the problem, thanks! — Reply to this email directly, view it on GitHub <#191>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OAZEDRO2IAYMNV4J6TVJJCNJANCNFSM5VRI4GUA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[sakhdbx]

thanks for your reply!
However, when i use table_annovar with -vcfinput, the sample id in the header has changed, and the number of 'otherinfo's is not equal to my sample number, i can not match the sample id with the annotation information. The sample id is important for me to know their cilinical information.
Before annotation:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1003387 1006225 1006276 1006950 1006996 1014654 ...
After annotation:
#Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene
cytoBand ExAC_ALL ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS avsnp147 SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_pred MutationTaster_score MutationTaster_pred MutationAssessor_score MutationAssessor_pred FATHMM_score FATHMM_pred PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_phred DANN_score
fathmm-MKL_coding_score fathmm-MKL_coding_pred MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred integrated_fitCons_score integrated_confidence_value GERP++_RS phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_vertebrate
phastCons20way_mammalian SiPhy_29way_logOdds Otherinfo1 Otherinfo2 Otherinfo3 Otherinfo4 Otherinfo5 Otherinfo6 Otherinfo7 Otherinfo8 Otherinfo9 Otherinfo10 ...
@kaichop