gravatar for cchyn.chua

2 hours ago by

Dear hive,

I am rather new to bioinformatics and am hoping to seek some advice.

I have trying to annotate the vcf output file obtained from VarScan using ANNOVAR, however have not been successful. The error code that I receive is as follows:

Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chrom position="" ref="" cons="" reads1reads2="" varfreq="" strands1="" strands2="" qual1="" qual2="" pvalue="" mapqual1="" mapqual2="" reads1plus="" reads1minus="" reads2plus="" reads2minus="" varallele="">
Error running system command: <convert2annovar.pl -includeinfo="" -allsample="" -withfreq="" -format="" vcf4="" users="" chynchua="" desktop="" shelltest="" idt_20201203="" results="" variant_calling="" ae_may18.raw.vcf="" &gt;="" myanno.avinput="">

It seemed that the initial output vcf format from VarScan is not compatible with ANNOVAR (as it does not come with an INFO string etc?)? Is there an interim step that I should do prior to using ANNOVAR? or is there something I could have changed with my VarScan options that could rectify this?

Will greatly appreciate any suggestions and advice on how I can proceed

thanks!



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