Open sakhdbx opened 2 years ago
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.
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!
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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:
After annotation:
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
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!