How can I view result of SNPs (called by samtools) as the output vcf file is very big and difficult to open? Any suggestions!
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Thanks, -
Well, if you want to view and inspect the VCF file directly, UNIX text viewing tools such as the 'less' command are good. If you want you can make things easier on the eye by for example first cutting out only those columns you are interested in for the moment (for example: cut -f 1,4,5,9 file.vcf | less).
Depending on what exactly you want to look at, you can also import the VCF file into a genome browser such as IGV and see the locations of the called SNPs displayed in a track along the genome.
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