Annovar warning message

Question

[hdtms]

I'm using Annovar for variant annotation I want to input a vcf file and I get this warning message:

#perl convert2annovar.pl Indel_Autoss.vcf -format vcf4 > Indel_Aut_Ann.vcf4
WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead.
NOTICE: Finished reading 17485 lines from VCF file
NOTICE: A total of 17279 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 18024 indels/substitutions
NOTICE: Finished writing 0 SNP genotypes (0 transitions and 0 transversions) and 3390 indels/substitutions for 1 sample (but input contains 70 samples)
WARNING: 125 invalid alternative alleles found in input file

I don't know what the warning message means, is it an error on the file?

Answer 1

[h.mon]

Read Annovar faq 6