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Vt (view source)

Revision as of 01:03, 2 March 2018

353 bytes added ,  01:03, 2 March 2018
→‎Mac
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   </div>
 
   </div>
   −
Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
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=== Mac ===
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Some features of C++11 is used, thus there is a need for newer versions of gcc and clang.
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 +
  You will need to install the package xz prior to installing vt.
   −
== Mac ==
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  homebrew install xz
   −
You may also install vt on mac via homebrew.
     −
  brew install homebrew/science/vt
+
Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
 +
Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.
    
= Updating =
 
= Updating =
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<div class=" mw-collapsible mw-collapsed">
 
<div class=" mw-collapsible mw-collapsed">
−
   #converts in.bcf to tab format with selected INFO fields
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   #converts in.bcf to tab format with selected INFO and FILTER fields
−
   vt info2tab in.bcf -v -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
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   vt info2tab in.bcf -u PASS -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
−
 
   
   <div style="height:6em; overflow:auto; border: 2px solid #FFF">
 
   <div style="height:6em; overflow:auto; border: 2px solid #FFF">
 +
  INPUT
 +
  =====
 
   20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR
 
   20 17548608 . A AC . PASS CENTERS=vbi;NCENTERS=1;OLD_MULTIALLELIC=20:17548598:GAAAAAAAAAAAAA/GAAAAAAAAAAAA/GAAAAAAAAAAAAAA/GAAAAAAAAAA/GAAAAAAAAAAA/GAAAAAAAAAACAAA;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAACAAAG;EX_MOTIF=C;EX_MLEN=1;EX_RU=C;EX_BASIS=C;EX_BLEN=1;EX_REPEAT_TRACT=17548608,17548609;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=2;EX_RL=2;EX_LL=3;EX_RU_COUNTS=0,2;EX_SCORE=0;EX_TRF_SCORE=-14;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=14;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[A]AAAGAAGGAA;MDUST;LOBSTR
 
   20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA
 
   20 17548608 . AAAAG A . PASS CENTERS=ox1;NCENTERS=1;EX_MOTIF=AAAG;EX_MLEN=4;EX_RU=AAAG;EX_BASIS=AG;EX_BLEN=2;EX_REPEAT_TRACT=17548609,17548612;EX_COMP=100,0,0,0;EX_ENTROPY=0;EX_ENTROPY2=0;EX_KL_DIVERGENCE=2;EX_KL_DIVERGENCE2=4;EX_REF=0.75;EX_RL=4;EX_LL=4;EX_RU_COUNTS=0,1;EX_SCORE=0.75;EX_TRF_SCORE=-1;FZ_MOTIF=A;FZ_MLEN=1;FZ_RU=A;FZ_BASIS=A;FZ_BLEN=1;FZ_REPEAT_TRACT=17548599,17548611;FZ_COMP=100,0,0,0;FZ_ENTROPY=0;FZ_ENTROPY2=0;FZ_KL_DIVERGENCE=2;FZ_KL_DIVERGENCE2=4;FZ_REF=13;FZ_RL=13;FZ_LL=13;FZ_RU_COUNTS=13,13;FZ_SCORE=1;FZ_TRF_SCORE=26;FLANKSEQ=GAAAAAAAAA[AAAAG]AAGGAACTAC;MDUST;LOBSTR;OLD_VARIANT=20:17548598:GAAAAAAAAAAAAAG/GAAAAAAAAAA
−
   
   </div>
 
   </div>
−
 
+
  OUTPUT
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   CHROM POS   REF   ALT N_ALLELE  EX_RL  FZ_RL MDUST LOBSTR VNTRSEEK  RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
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  ======
−
   20 17548608  A   AC 2        2 13 1 1 0   0    17548608                17548608
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   CHROM POS   REF   ALT N_ALLELE PASS EX_RL  FZ_RL MDUST LOBSTR VNTRSEEK  RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
−
   20 17548608  AAAAG  A 2        4      13     1 1      0        0    17548609                17548609
+
   20 17548608  A   AC 2        1    2     13 1 1 0   0    17548608                17548608
 +
   20 17548608  AAAAG  A 2        1    4      13       1       1      0        0    17548609                17548609
    
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
   usage : vt info2tab [options] <in.vcf>
 
   usage : vt info2tab [options] <in.vcf>
 
    
 
    
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   options : -v  print variant CHROM,POS,REF,ALT,N_ALLELE [false]
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   options : -d  debug [false]
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            -d  debug [false]
   
             -f  filter expression []
 
             -f  filter expression []
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             -t  list of info tags to be extracted []
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             -u  list of filter tags to be extracted []-t  list of info tags to be extracted []
 
             -o  output tab delimited file [-]
 
             -o  output tab delimited file [-]
 
             -I  file containing list of intervals []
 
             -I  file containing list of intervals []
Line 1,064: Line 1,065:  
   vt profile_mendelian vt.genotypes.bcf -p trios.ped -x mendel
 
   vt profile_mendelian vt.genotypes.bcf -p trios.ped -x mendel
   −
   pedigree file format is described in [http://csg.sph.umich.edu//abecasis/merlin/tour/input_files.html here]
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   pedigree file format is described in [[Vt#Pedigree File|here]].
    
   #this is a sample output for mendelian error profiling.
 
   #this is a sample output for mendelian error profiling.
Line 1,097: Line 1,098:  
   no. of trios    : 2
 
   no. of trios    : 2
 
   no. of variants  : 25346
 
   no. of variants  : 25346
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  −
   
    
 
    
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
Line 1,115: Line 1,114:  
  </div>
 
  </div>
 
</div>
 
</div>
−
      
=== Profile SNPs ===
 
=== Profile SNPs ===
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= Pedigree File =
 
= Pedigree File =
   −
   vt understands an augmented version introduced by [hmkang@umich.edu Hyun] of the PED described by [http://zzz.bwh.harvard.edu/plink/data.shtml#ped plink].
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   vt understands an augmented version introduced by [mailto:hmkang@umich.edu Hyun] of the PED described by [http://zzz.bwh.harvard.edu/plink/data.shtml#ped plink].
 
   The pedigree file format is as follows with the following mandatory fields:
 
   The pedigree file format is as follows with the following mandatory fields:
 +
       
 
{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
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! scope="col"| Description
 
! scope="col"| Description
 
! scope="col"| Valid Values
 
! scope="col"| Valid Values
 +
! scope="col"| Missing Values
 
|-
 
|-
 
|Family ID<br>
 
|Family ID<br>
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Phenotype
 
Phenotype
 
|ID of this family <br>
 
|ID of this family <br>
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ID of this individual <br>
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ID(s) of this individual (comma separated) <br>
 
ID of the father <br>
 
ID of the father <br>
 
ID of the mother <br>
 
ID of the mother <br>
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Sex of the individual.  <br>
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Sex of the individual<br>
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Phenotype.
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Phenotype  
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|[A-Za-z_]+<br>
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|[A-Za-z0-9_]+<br>
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[A-Za-z_]+ <br>
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[A-Za-z0-9_]+(,[A-Za-z0-9_]+)* <br>
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[A-Za-z_]+ <br>
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[A-Za-z0-9_]+ <br>
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[A-Za-z_]+<br>
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[A-Za-z0-9_]+<br>
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1 = male, 2 = female and other = alternative<br>
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1=male, 2=female, other, male, female<br>
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[A-Za-z_]+
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[A-Za-z0-9_]+
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|  0 <br>
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cannot be missing <br>
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0 <br>
 +
0 <br>
 +
other<br>
 +
-9
 
|}
 
|}
   −
    Family ID
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  Examples:   
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     Individual ID
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−
     Paternal ID
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     ceu     NA12878    NA12891    NA12892    female    -9
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     Maternal ID
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     yri     NA19240    NA19239    NA19238    female   -9
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     Sex (1=male; 2=female; other=unknown)
  −
    Phenotype
     −
     ceu NA12878   NA12891 NA12892     female
+
     ceu     NA12878    NA12891     NA12892    2    -9
−
     yri      NA19240    NA19239    NA19238    female
+
     yri      NA19240    NA19239    NA19238    2    -9
   −
     ceu NA12878,NA12878A   NA12891 NA12892     female
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    #allows tools like profile_mendelian to detect duplicates and check for concordance
−
     yri      NA19240                             NA19239    NA19238    female
+
     ceu     NA12878,NA12878A    NA12891     NA12892    female   case
 +
     yri      NA19240             NA19239    NA19238    female   control
   −
     ceu NA12878,NA12878A   NA12891 NA12892     0
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    #allows tools like profile_mendelian to detect duplicates and check for concordance
−
     yri      NA19240                            NA19239     NA19238    0
+
     ceu     NA12412   0  0     female  case
 +
     yri      NA19650    0  0     female  control
    
= Resource Bundle =
 
= Resource Bundle =
Atks
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/14925...14996"

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