Conflict between mpileup/bcftools and GATK in VCF file

[ericarcher]

I'm using samtools mpileup | bcftools view to generate VCF files for reads mapped to a mitogenome reference. I would like to use the GATK VariantsToTable walker to create an importable table of the base distribution and qualities at each site. The problem I'm having is that for sites with coverage below 3 (DP=1 or DP=2), the VCF file that gets created has an 'X' in the ALT field rather than a '.'. When I put these files through GATK's VariantsToTable, I get the following error:

##### ERROR MESSAGE: The provided VCF file is malformed at line nmber 27: Unparsable vcf record with allele X

Here are some example lines from my VCF file:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT z0000064_mtdna-test
gi|170027011|gb|EU557096.1| 17 . T X 0.404 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=23;FQ=-8.25 GT:PLP:GQ 0/0:0,3,23:1:13
gi|170027011|gb|EU557096.1| 18 . T X 0.206 . DP=2;AF1=0;AC1=0;DP4=1,1,0,0;MQ=31;FQ=-10.9 GT:PLP:GQ 0/0:0,6,60:2:19
gi|170027011|gb|EU557096.1| 19 . T . 16.2 . DP=3;AF1=0;AC1=0;DP4=1,2,0,0;MQ=27;FQ=-13.7 PLP 0:3
gi|170027011|gb|EU557096.1| 20 . T . 16.2 . DP=3;AF1=0;AC1=0;DP4=1,2,0,0;MQ=27;FQ=-13.7 PLP 0:3