I analyse reads from Ion Torrent platform with bwa-samtools pipeline. I used them in such way:
bwa mem samtools view (convert sam to bam) samtoos sort samtools mpileup bcftools view -bvcg - > var.raw.bcf (call variants as I understand correctly) bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf (convert bcf to vcf)
And at the last stage I can't understand why do we set maximal read depth. Don't we exclude thereby many SNPs? By what SNPs with high read depth are bad?