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Old 06-19-2013, 02:01 AM   #1
sadiexiaoyu
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Location: Switzerland

Join Date: Apr 2013
Posts: 55
Default bcftools command not found

Hi, All,

I am trying to generate a consensus sequence using samtools. And I used the command as follow:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq >cns.fq

But I get the error:

-bash: bcftools: command not found
Use of uninitialized value $l in numeric lt (<) at /Users/samtools-0.1.19/For consensus sequence/vcfutils.pl line 545.
Use of uninitialized value $l in numeric lt (<) at /Users/samtools-0.1.19/For consensus sequence/vcfutils.pl line 545.


I saw bcftools sub-file in samtools file, but there is no bcftools file in the sub-file. Could anyone tell me what is wrong?

Best,

Sadiexiaoyu
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