Samtools Call Snps

Question

[GPR]

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

Answer 1

[Pierre Lindenbaum]

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/

Answer 2

[GPR]

Pierre: In the link you suggest, should I take that vcfutils.lua is the same as vcfutils.pl? Am I missing something? Thanks.

[Matteo]

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/