No it's different. Go to your samtools folder and look into bcftools subfolder.
Look here:
http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/samtools/bcftools/
Samtools Call Snps
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
2 answers
Yes, you can find those commands under the samtools installation folder, in the misc directory.
http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/samtools/misc/
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