How to assign the annovar annotation file to InterVar when skipping annovar?

[lincj1994]

Hi.
I have a variant dataset which has been annotated by Annovar. So I'd like to skip annovar when performing InterVar but it returned an error:

ERROR: The InterVar did not find the annotation result file from ANNOVAR!
ERROR: The name of annotation result file should be like /home/lcj/lincj/CBCGA/WES/InterVar-output/CBCGAWES_anno1*.hg19__multianno.

I have checked the help message of Intervar.py but there was no argument to assign the annotation file. So in the configure.ini.
Besides, no *.hg19_multianno file was found in the destination format.

[quanliustc]

suppose, your input file is test2.av and your Annovar ouput file name as: test4.av.hg19_multianno.txt; then you could run as: python Intervar.py -b hg19 -i test2.av --skip_annovar -o test4.av

[lincj1994]

Thanks for your reply. I have renamed the annovar output file and it worked for the first several variants. And it returned an error like this:

Traceback (most recent call last):
  File "Intervar.py", line 2122, in <module>
    main()
  File "Intervar.py", line 2091, in main
    sum2=my_inter_var(annovar_outfile)
  File "Intervar.py", line 1844, in my_inter_var
    intervar_bp=assign(BP,line,Freqs_flgs,Funcanno_flgs,Allels_flgs)
  File "Intervar.py", line 1715, in assign
    BP7=check_BP7(line,Funcanno_flgs,Allels_flgs)
  File "Intervar.py", line 1627, in check_BP7
    if float(cls[Funcanno_flgs['dbscSNV_RF_SCORE']])<0.6 and float(cls[Funcanno_flgs['dbscSNV_ADA_SCORE']])<0.6:
ValueError: could not convert string to float: 'X'

Probably is it because that InterVar cannot recognize chromosome X? But in the *multianno.txt.intervar file, some of the variants in chromosome X have also been annotated by InterVar.

[yinbinqiu]

hello, how do you solve this problem?