Changes

From Genome Analysis Wiki
Jump to navigationJump to search

Vt (view source)

Revision as of 11:14, 6 May 2015

365 bytes removed ,  11:14, 6 May 2015
→‎Partition
Line 558: Line 558:  
</div>
 
</div>
   −
=== Partition ===
+
=== Multi Partition ===
    
Partitions variants between 2 indexed VCF files.
 
Partitions variants between 2 indexed VCF files.
    
<div class=" mw-collapsible mw-collapsed">   
 
<div class=" mw-collapsible mw-collapsed">   
−
   #partitions all variants in bi1.bcf  and bi2.bcf
+
   #partitions variants 3 way
−
  vt partition bi1.bcf bi2.bcf
+
  vt multi_partition hc.genotypes.bcf  pl.genotypes.bcf st.genotypes.bcf
   −
   Options:    input VCF file a  bi1.bcf
+
   Options:    input VCF file a  hc.genotypes.bcf
−
               input VCF file b  bi2.bcf <br>
+
               input VCF file b  pl.genotypes.bcf
−
    A:      504676 variants
+
              input VCF file c  st.genotypes.bcf
−
    B:    1389333 variants <br>
  −
                  ts/tv  ins/del
  −
    A-B      37564 [0.19] [1.34]
  −
    A&B    467112 [1.55] [0.72]
  −
    B-A    922221 [1.20] [0.58]
  −
    of A    92.6%
  −
    of B    33.6%
     −
  #partitions only passed variants in bi1.bcf and bi2.bcf
+
      A:      97274 variants
−
  vt partition bi1.bcf bi2.bcf -f PASS
+
      B:      95458 variants
 +
      C:      98943 variants
   −
  Options:    input VCF file a  bi1.bcf
+
      A--      3887 [1.10] [0.86]
−
              input VCF file b  bi2.bcf
+
      -B-      7890 [1.45] [0.98]
−
              [f] filter            PASS <br>
+
      AB-       4360 [0.99] [1.32]
−
    A:      466148 variants
+
      --C      8277 [1.75] [2.21]
−
    B:      986056 variants <br>
+
      A-C      7458 [1.78] [0.49]
−
                  ts/tv  ins/del
+
      -BC      1639 [1.63] [1.03]
−
    A-B      47261 [0.44] [1.36]
+
      ABC      81569 [2.28] [1.08]
−
    A&B    418887 [1.80] [0.68]
  −
    B-A    567169 [1.43] [0.72]
  −
    of A    89.9%
  −
    of B    42.5%
      
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
   −
partition v0.5
+
   usage : vt multi_partition [options] <in1.vcf><in2.vcf>...
−
 
  −
description : partition variants. check the overlap of variants between 2 data sets.
  −
 
  −
   usage : vt partition [options] <in1.vcf><in2.vcf>
  −
 
   
   options : -f  filter
 
   options : -f  filter
 
             -I  file containing list of intervals []
 
             -I  file containing list of intervals []
Atks
1,102

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13189"

Navigation menu