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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)<br>
FS/NFS : 0.66 (67/35) //Proportion of frameshift Indels. (#Frameshift Indels/#Nonframeshift Indels)<br>
dbsnp
dbsnp //A represents the data set you input, B represents dbsnp
A-B 2975 [1.06]
A-B 2975 [1.06] //#variants in A only [ins/del ratio]
A&B 5929 [0.86]
A&B 5929 [0.86] //#variants in A and B
B-A 2059845 [1.51]
B-A 2059845 [1.51]
Precision 66.6%
Precision 66.6% //A&B/A this represents how novel your data set is in the variants represented.
Sensitivity 0.3% <br>
Sensitivity 0.3% //A&B/B this represents sensitivity somewhat if dbsnp is considered a high quality Indel
//set and the sample are the same in both data sets. (which they usually are not, this is still
//nonetheless a useful indicator)<br>
mills
mills
A-B 5705 [0.81]
A-B 5705 [0.81]
* Annotation of STRs is really important. Show example of a deceptive single base pair variant
* Annotation of STRs is really important. Show example of a deceptive single base pair variant
* Mendelian analysis
* AFS
* Can check concordance of genotypes between callers - partitiion
* Can check concordance of genotypes between callers - partitiion
* Type of Indels - homopolymer types and STR types and isolated, Adjacent SNPs ,Adjacent MNPs,Clumping variants
* Type of Indels - homopolymer types and STR types and isolated, Adjacent SNPs ,Adjacent MNPs,Clumping variants
