REQUIRED for all errors and issues:
a) GATK version used: 4.01.1
b) Exact command used: 
c) Entire program log:

A few years ago, I had used the the off-label workflow for Mutect2 to find somatic differences in clonally derived plant tissue with RNAseq. I had really good success with it and I am now running this pipeline again. Because it is not a model, I have to generate my own germline resource file to run Mutect2 and it requires manual edits. However, when I attempt to use ValidateVariants to turn my manually modified VCF into a working one with an index file, I get the one of the following errors.

Error - 1. "No suitable codecs found" OR Error - 2. "The provided VCF file is malformed at approximately line number 2561: unparsable vcf record with allele A" 

Steps I used to create these files were:

1. Convert vcf from 1st pass of Mutect2 to a table

/home/jschwoch/stow/gatk-4.0.1.1/gatk VariantsToTable -V /scratch/jschwoch/1RG_MT.vcf -F CHROM -F POS -F ID -F REF -F ALT -F TLOD -GF QUAL -GF AF -O /scratch/jschwoch/1RG_MT.table

2. Modify in excel

 =CONCATENATE("TLOD=",F2," ; AF=",H2)

Add # in front of CHROM
Copy-Paste column in-column as values
Copy contents to a text editor and remove trailing white spaces
Save as a text file. For example: "Aaf.table"

3. Create a new header then manually edit

cat /scratch/jschwoch/1RG_MT.vcf | grep '##' > /vol/share/cruzan_lab/Jaime/1RG_MT.header

While in nano mode Manually change FORMAT to INFO
Use CTRL + K to delete unnecessary lines

4. Concatenate the edited header to the edited table

cat /vol/share/cruzan_lab/Jaime/clonal_rna/Mutect2_passes/VCF_headers/1RG_MT.header /vol/share/cruzan_lab/Jaime/clonal_rna/Mutect2_passes/vcf_table/1RG_MT.table > /vol/share/cruzan_lab/Jaime/clonal_rna/Mutect2_passes/vcf_table/1_manmod.vcf

5. ValidateVariants to create an index file

/home/jschwoch/stow/gatk-4.0.1.1/gatk ValidateVariants -V /scratch/jschwoch/clonal_rna/1_manmod.vcf

I can't seem to figure out why these manual edits all used to work but no longer do. 

When I open the VCF and go to the Line it is reporting an unparsable VCF record, I only notice that is is the first SNP in the file that has two alternate allele options.

• Error - 2. "The provided VCF file is malformed at approximately line number 2561: unparsable vcf record with allele A" 

For example: It seems to be having a problem with variants shown below