connsensus file too big to read

Question

[jamessemaj712]

Hi,

I am trying to use soapsnp.Ion chromosme 22 oh human38.I did all the steps for generating the consensus filr using soap snp to find if there are any snps in the consensus file.The problem is my consensus file is 2.7GB in size which is not opening in computer i.e. my laptop hangs and also it is not possible for me to search for snp sites. Is there any graphical viewer or something of similar sort to view the snp sites in my consensus file?

[Matt Shirley]

You should explain what you are doing specifically. Are you trying to open your sequence in a text editor such as Notepad? If so you'll run out of memory. If you're on Windows there's probably a better solution but if you're on Mac or Linux try using less in a terminal. Google is your friend here.

[jamessemaj712]

How can I locate the snp in such a big consensus file.I even don't know if there exists a snp?

[Matt Shirley]

I think you're supplying some parameters incorrectly because the output format section of the manual suggests a 17-column format where each line is a SNP. The manual is ambiguous and this could be one line for each position on chr22, which would explain your huge file size. If this is the case you could find mismatches between columns 3 and 4 using something like awk '{if ($3 != $4) print}' < consensus.txt. However, SOAP is a very old tool, and you might consider using something more recent for resequencing and calling SNPS, like GATK or Freebayes.