Changes

== Comparison with other data sets ==

== Comparison with other data sets ==

It is usually useful to examine the call sets against known data sets.

It is usually useful to examine the call sets against known data sets for the passed variants.

   vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt  -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS"

   vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt  -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS"

   data set

   data set

     No Indels        :        613 [0.72]

     No Indels        :        613 [0.72]

       FS/NFS        :      0.50 (2/2)

       FS/NFS        :      0.50 (2/2) #frame shift / non frameshift indels proportion, the bracket gives the counts of the frame shift and non frameshift indels

       Low complexity :      0.46 (283/613) <br>

       Low complexity :      0.46 (283/613) #fraction of indels in low complexity region, the bracket gives the counts of the indels <br>

   1000G

   1000G #1000 Genomes Phase 1 data set

     A-B        371 [0.76]

     A-B        371 [0.76]   #variants found in data set only

     A&B        242 [0.66]

     A&B        242 [0.66] #variants found in both data sets

     B-A        276 [0.89]

     B-A        276 [0.89] #variants found in 1000G phase 1 data set only

     Precision    39.5%

     Precision    39.5% #39.6% of the call set are previously known, so 60.5% are novel variants.

     Sensitivity  46.7% <br>

     Sensitivity  46.7% #sensitivity of variant calling, 46,7% of known variants from 1000 Genomes were rediscovered  <br>

   mills

   mills #Mills et al. data set

     A-B        542 [0.68]

     A-B        542 [0.68]

     A&B        71 [1.03]

     A&B        71 [1.03]

     B-A        31 [1.07]

     B-A        31 [1.07]

     Precision    11.6%

     Precision    11.6%

     Sensitivity  69.6% <br>

     Sensitivity  69.6% <br>

   dbsnp

   dbsnp # Indels from dbSNP

     A-B        405 [0.68]

     A-B        405 [0.68]

     A&B        208 [0.79]

     A&B        208 [0.79]

* dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly.  But assuming most are real, then precision is a useful estimated quantity from this reference data set.

* dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly.  But assuming most are real, then precision is a useful estimated quantity from this reference data set.

* Mills:  contains doublehit common indels from the Mills. et al paper and is a relatively good measure of sensitivity for common variants.  Because not all Indels in this set is expected to be present in your sample, this actually gives you an underestimate of sensitivity.

* Mills:  contains doublehit common indels from the Mills. et al paper and is a relatively good measure of sensitivity for common variants.  Because not all Indels in this set is expected to be present in your sample, this actually gives you an underestimate of sensitivity.

   vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt  -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS"

   vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt  -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS"

     Precision    4.7%

     Precision    4.7%

     Sensitivity  0.7%

     Sensitivity  0.7%

This analysis supports filters too.

This analysis supports filters too.