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Old 09-27-2011, 03:03 PM   #1
Vilhelm84
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Default SAMtools VIM error

Howdy,
I am currently in the midst of my first deep-seq analysis. I am trying to pull my sequence variants out of my tophat alignment, however, the command I am using in samtools is not working and I am not sure why.

: samtools mpileup -uf fasta.fa accepted_hits.bam | view -bcg - > var.raw.bcf

This command line gives me this error:

Vim: Warning: Output is not to a terminal

and my terminal is locked up and I have to ctrl-z to get out. It seems the problem is the "-" command, but when I try to run this without that I get two errors:

Vim: Warning: Output is not to a terminal
Vim: Warning: Input is not from a terminal

My next step would be to pipe the .bcf file to vcfutils and filter to make a .vcf file and analyze from there but I am having trouble figuring out exactly what is wrong with the first step...any help?
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Old 09-27-2011, 04:29 PM   #2
nilshomer
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Try:
samtools mpileup -uf fasta.fa accepted_hits.bam | bcftools view -bcg - > var.raw.bcf
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Old 09-27-2011, 05:21 PM   #3
Vilhelm84
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Thanks, however I now get the error:
-bash: bcftools: command not found
I saw your previous thread regarding this and it seems that I need to recompile. I will do that and try again.
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Old 09-27-2011, 05:40 PM   #4
nilshomer
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bcftools comes with samtools.
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