I'm doing samtools mpileup snp calling but samtools is not including reads that are improperly paired or mates unmapped when I examine the snps using the bam file. Due to the nature of the reference I have I want to turn this behavior off. Turning quality scores filters for base and reads do not have an effect. Any ideas how to do this, or a snp caller that can set to include reads that are improperly paired to the snp calling process?
samtools mpileup -I -q 20 -Q 20 -DSuf Triticum_aestivum.IWGSP1.21.dna.genome.fa A6_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.bam C6_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.bam D3_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.bam| bcftools view -bvcg - > A6C6D3_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.bcf bcftools view A6C6D3_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.bcf | ./vcfutils.pl varFilter -D100 > A6C6D3_P33_Triticum_aestivum.IWGSP1.20.dna.genome_novo_H15_t60.sort.rmdup.vcf