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Revision as of 12:35, 3 September 2015

188 bytes removed ,  12:35, 3 September 2015
→‎Profile SNPs
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=== Profile SNPs ===
 
=== Profile SNPs ===
   −
Profile Indels.  The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
+
Profile SNPs.  The reference data sets can be obtained from [[Vt#Resource_Bundle|vt resource bundle]].
    
<div class=" mw-collapsible mw-collapsed">
 
<div class=" mw-collapsible mw-collapsed">
−
   #profile indels found in mills.vcf
+
   #profile snps found in 20.sites.vcf
−
   vt profile_indels -g indel.reference.txt mills.vcf -r hs37d5.fa  -i 20
+
   vt profile_snps -g snp.reference.txt 20.sites.vcf -r hs37d5.fa  -i 20
    
   #this is a sample output for indel profiling.
 
   #this is a sample output for indel profiling.
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   # for the FS/NFS field, that is the proportion of coding indels that are frame shifted.   
 
   # for the FS/NFS field, that is the proportion of coding indels that are frame shifted.   
 
   # The numbers in curved bracket are the counts of frame shift and non frame shift indels respectively.
 
   # The numbers in curved bracket are the counts of frame shift and non frame shift indels respectively.
−
  data set
+
  data set
−
    No Indels :     46974 [0.89]
+
    No. SNPs          :     508603 [2.09]
−
      FS/NFS :      0.26 (8/23) <br>
+
        SYN/NONSYN    :      1.00 (4617/0)
 +
        Low complexity :      0.08 (39837/508603) <br>
 +
  1000g
 +
    A-B    109970 [1.39]
 +
    A&B    398633 [2.37]
 +
    B-A    1340682 [2.26]
 +
    Precision    78.4%
 +
    Sensitivity  22.9% <br>
 
   dbsnp
 
   dbsnp
−
     A-B     30704 [0.92]
+
     A-B    324063 [1.99]
−
     A&B      16270 [0.83]
+
     A&B    184540 [2.29]
−
    B-A    2049488 [1.52]
+
     B-A    103893 [2.60]
−
    Precision    34.6%
+
     Precision   36.3%
−
    Sensitivity  0.8% <br>
+
     Sensitivity 64.0%
−
  mills
  −
     A-B     43234 [0.88]
  −
     A&B      3740 [1.00]
  −
     B-A    203278 [0.98]
  −
     Precision     8.0%
  −
    Sensitivity  1.8% <br>
  −
  mills.chip
  −
    A-B      46847 [0.89]
  −
    A&B        127 [0.90]
  −
    B-A      8777 [0.93]
  −
    Precision    0.3%
  −
     Sensitivity   1.4% <br>
  −
  affy.exome.chip
  −
    A-B      46911 [0.89]
  −
    A&B        63 [0.43]
  −
    B-A      33997 [0.47]
  −
    Precision    0.1%
  −
    Sensitivity  0.2% <br>
      
   # This file contains information on how to process reference data sets.
 
   # This file contains information on how to process reference data sets.
 +
  #
 
   # dataset - name of data set, this label will be printed.
 
   # dataset - name of data set, this label will be printed.
−
   # type    - True Positives (TP) and False Positives (FP).
+
   # type    - True Positives (TP) and False Positives (FP)
−
   #          overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively.
+
   #          overlap percentages labeled as (Precision, Sensitivity) and (False Discovery Rate, Type I Error) respectively
−
   #        - annotation.
+
   #        - annotation
−
   #          file is used for GENCODE annotation of frame shift and non frame shift Indels.
+
   #          file is used for GENCODE annotation of frame shift and non frame shift Indels
−
   # filter  - filter applied to variants for this particular data set.
+
   # filter  - filter applied to variants for this particular data set  
−
   # path    - path of indexed BCF file.
+
   # path    - path of indexed BCF file
−
   #dataset     type           filter                       path
+
   #dataset               type             filter                                 path
−
   1000g       TP             N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/1000G.snps_indels.sites.bcf
+
   1000g                 TP               N_ALLELE==2&&VTYPE==SNP                /net/fantasia/home/atks/ref/vt/grch37/1000G.v5.snps.indels.complex.svs.sites.bcf
−
  mills        TP              N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/mills.208620indels.sites.bcf
+
   dbsnp                 TP               N_ALLELE==2&&VTYPE==SNP                /net/fantasia/home/atks/ref/vt/grch37/dbSNP138.snps.indels.complex.sites.bcf
−
   dbsnp       TP             N_ALLELE==2&&VTYPE==INDEL    /net/fantasia/home/atks/ref/vt/grch37/dbsnp.13147541variants.sites.bcf
+
   GENCODE_V19           cds_annotation   .                                     /net/fantasia/home/atks/ref/vt/grch37/gencode.v19.cds.bed.gz
−
   GENCODE_V19 cds_annotation .                           /net/fantasia/home/atks/ref/vt/grch37/gencode.cds.bed.gz
+
   DUST                   cplx_annotation .                                     /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz
−
   DUST         cplx_annotation .                           /net/fantasia/home/atks/ref/vt/grch37/mdust.bed.gz
      
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
−
   usage : vt profile_indels [options] <in.vcf>
+
   usage : vt profile_snps [options] <in.vcf>
   −
   options : -g  file containing list of reference datasets []
+
   options : -f  filter expression []
 +
            -g  file containing list of reference datasets []
 
             -I  file containing list of intervals []
 
             -I  file containing list of intervals []
 
             -i  intervals []
 
             -i  intervals []
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  </div>
 
  </div>
 
</div>
 
</div>
−
      
=== Profile Indels ===
 
=== Profile Indels ===
Atks
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13696"

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