A vcf file processed after those 3 commands below seems has filtered low-phred polymorphic bases. What is the default threshold? Where can I change that threshold in command?
$samtools mpileup -uf Sorbil.fasta sample.bam > sample.pileup
$bcftools view -bvcg ample.pileup > var.bcf
$bcftools view var.bcf > var.vcf
$samtools mpileup -uf Sorbil.fasta sample.bam > sample.pileup
$bcftools view -bvcg ample.pileup > var.bcf
$bcftools view var.bcf > var.vcf