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The VCF format is a simple text format. It starts with several header lines, which all start with the two '##' characters, and is followed by a single line per marker that provides both summary information about the marker and genotypes for each individual. You can review the contents of the VCF file using the 'more' command:
The VCF format is a simple text format. It starts with several header lines, which all start with the two '##' characters, and is followed by a single line per marker that provides both summary information about the marker and genotypes for each individual. You can review the contents of the VCF file using the 'more' command:
more mpileup/chr20.mpileup.vcf
more result/chr20.mpileup.vcf
Here are some questions for you to investigate:
Here are some questions for you to investigate:
* How many variant sites were detected in this dataset? Try a command like this one:
* How many variant sites were detected in this dataset? Try a command like this one:
grep -vE ^# chr20.mpileup.vcf | wc -l
grep -vE ^# result/chr20.mpileup.vcf | wc -l
(The grep command line excludes all lines beginning with # and then the wc command counts the number of lines in the file).
(The grep command line excludes all lines beginning with # and then the wc command counts the number of lines in the file).
