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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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NOTICE: output files will be written to .<samplename>.avinput， cannot write to outfile #191

Open sakhdbx opened 2 years ago

sakhdbx commented 2 years ago

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 commented 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!

— Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/191, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OAZEDRO2IAYMNV4J6TVJJCNJANCNFSM5VRI4GUA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

sakhdbx commented 1 year ago

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