Hello, I have a rather naive question.
Given the two command-lines found below, can somebody tell me if "samtools.pl and vcfutils.pl are part of the samtools package? Do I need to instal them separately?
samtools.pl varFilter raw.pileup | awk '$6>=20' > final.pileup
samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
Thanks in advance. GP