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?
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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