Question: Samtools Call Snps
1
gravatar for GPR
8.6 years ago by
GPR320
Mexico
GPR320 wrote:

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

snp • 3.0k views
ADD COMMENTlink written 8.6 years ago by GPR320
3
gravatar for Pierre Lindenbaum
8.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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/

ADD COMMENTlink written 8.6 years ago by Pierre Lindenbaum133k
0
gravatar for GPR
8.6 years ago by
GPR320
Mexico
GPR320 wrote:

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

ADD COMMENTlink written 8.6 years ago by GPR320
1

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/

ADD REPLYlink modified 8.6 years ago • written 8.6 years ago by Matteo200
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