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=Tools=
=Tools=
This walkthrough requires [[vt|vt]].
=Analyses=
=Analyses=
The file generated from the indel calling is a binary version [[http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2 BCFv2.1]] of the Variant Call Format (VCF). BCFv2.1 is more efficient to process as the data is already stored in computer readable format on the hard disk. It is however not necessarily more compact than VCF4.2 especially when the format fields are rich in details.
==File Preparation==
==File Preparation==
To convert to BCF format which will work fast with vt:
To convert to BCF format which will work fast with vt:
vt view mills.vcf -o mills.bcf
vt view mills.vcf -o mills.bcf
data set
data set
No Indels : 8904 [0.93]
No Indels : 8904 [0.93] //#variants in your data set [ins/del ratio]
FS/NFS : 0.66 (67/35) //Proportion of frameshift Indels. (#Frameshift Indels/#Nonframeshift Indels)<br>
FS/NFS : 0.66 (67/35) //Proportion of frameshift Indels. (#Frameshift Indels/#Nonframeshift Indels)<br>
dbsnp //A represents the data set you input, B represents dbsnp
dbsnp //A represents the data set you input, B represents dbsnp
