TABLE 2.

Troubleshooting table.

Step	Problem	Possible reason	Solution
2A(ii)	You see ‘Failed’ for all the files to be downloaded	Internet connection or firewall settings issue	Please check your internet connection and firewall settings
2A(iii)	You see ‘ERROR’ information displayed	The wrong command was entered, or some required databases are not downloaded properly	Please check the log printed in the terminal. First, make sure that you typed in or pasted exactly the same command as written. If the command is correct, it is possible that one or more databases are not downloaded properly. You should find the missing database from the log and go back to Step 2A(ii) to download the missing database
2B(i), 2B(ii)	You see ‘ERROR’ about missing FASTA file	ANNOVAR cannot read the sequence files in the entered directory correctly	In this case, the ‘–seqfile <genome fasta file>’ argument should be used instead of the ‘—seqdir’ argument, to explicitly specify the genome FASTA file to be used
2C(v)	There are 0 variants in the final result in the ‘ANNOVAR filtering result’ section	The filter and model selected may be too stringent in this step	Please choose ‘Dominant model’ rather than ‘Recessive model’; please increase the MAF value to include more variants. Please note that filters and models do not affect the output in the ‘Basic Information’ section
2C(vi)	There is an error message right after you click ‘Submit’	The uploaded variant file is different from the ‘Input Format’ selection	For VCF, please make sure that the VCF file conforms to a valid format. VCF files can be validated with VCF tools60 (see http://vcftools.sourceforge.net/perl_module.html#vcf-validator)