Hello all,
I'm having trouble using samtools to get a consensus of a small viral genome and I'm fairly certian its user error. I am very new to all of this however I have not found my issue in the forum so here goes. If someone has posted this answer before and I didn't do a good enough job searching I would be very appreicative if you could link the response to this post.
I'm using mpileup to extract a consensus with the command listed in the documentation
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
(with my files in the places of ref.fa and aln.bam)
and I get "vcfutils.pl command not found" error.
I did some digging and found a post saying add perl to the command line before vcfutils
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq > cns.fq
and now I get "Can't open perl script "vcfutils.pl": No such file or directory" error.
I did some more digging and found a post from vcftools that says to use cpan, which I did and it ran fine, no errors and then re-ran the code with "perl" in and out of the line and I still get the same errors.
Can anyone think of a package that I missed or has someone defeated this problem and can help me with some insight?
I'm having trouble using samtools to get a consensus of a small viral genome and I'm fairly certian its user error. I am very new to all of this however I have not found my issue in the forum so here goes. If someone has posted this answer before and I didn't do a good enough job searching I would be very appreicative if you could link the response to this post.
I'm using mpileup to extract a consensus with the command listed in the documentation
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
(with my files in the places of ref.fa and aln.bam)
and I get "vcfutils.pl command not found" error.
I did some digging and found a post saying add perl to the command line before vcfutils
samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | perl vcfutils.pl vcf2fq > cns.fq
and now I get "Can't open perl script "vcfutils.pl": No such file or directory" error.
I did some more digging and found a post from vcftools that says to use cpan, which I did and it ran fine, no errors and then re-ran the code with "perl" in and out of the line and I still get the same errors.
Can anyone think of a package that I missed or has someone defeated this problem and can help me with some insight?
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