Pileup Haploid Base Calling, Creating Consensus Sequence

Question

[Lee Katz]

Hi all, I couldn't find if this has been asked here. I realize that samtools assumes that you are working with a diploid and will output heterozygous snps. How could I modify my script to make it not output heterozygous snps? In other words, how do I trick it into thinking that it is looking at a haploid genome? My snippet of code is in Perl and uses a command() subroutine which runs a string and prints the command to the screen.

command("samtools mpileup -uf $$settings{assembly} $bam > $out1");
command("bcftools view -cg - < $out1 > $out2");
command("vcfutils.pl vcf2fq -d $minDepth -D $maxDepth < $out2 > $fastqOutNonstandard");
command("vcfutils.pl varFilter -d $minDepth -D $maxDepth < $out2 > $variantsFile");

[Lee Katz]

Is there perhaps something like GATK which could do it instead?