I'm running samtools (version 1.3.1, Ubuntu 17.04 default) to generate a VCF from a reference and some BAM files:
samtools mpileup --ff 0x800 -r my_contig -v -f my_genome.fa *.bam -o my.vcf
But in the VCF file, all lines have a format like:
my_contig 4 . A <*> 0 . DP=1;I16=1,0,0,0,34,1156,0,0,0,0,0,0,0,0,0,0;QS=1,0;MQ0F=1 PL 0,0,0 0,3,4
In short, ALT (alternative allele) is set to be "<>". From the VCF specification, * indicates a deletion, while brackets indicate some sort of ID string. To me, none of these make much sense, and here the depth is 1 - how can there be any variants here? (For actual polymorphic sites, ALT is something like G,<>. As if that helps.)
I'm quite confused by this, and a subsequent 'bcftools' similarly fails:
Symbolic alleles other than <DEL> are currently not supported: <*> at my_contig:4
I can generate the consensus using a program I've written myself, but I would like to leverage whatever magic bcftools uses to QC polymorphisms, and also I think it is better to stick to more mainstream tools - providing they work, that is.