Question: Annovar warning message
0
gravatar for hdtms
16 months ago by
hdtms 20
hdtms 20 wrote:

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?

warning annovar • 699 views
ADD COMMENTlink modified 16 months ago by h.mon24k • written 16 months ago by hdtms 20
1
gravatar for h.mon
16 months ago by
h.mon24k
Brazil
h.mon24k wrote:

Read Annovar faq 6

ADD COMMENTlink written 16 months ago by h.mon24k
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