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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>
| + | === Mac === |
− | Some features of C++11 is used, thus there is a need for newer versions of gcc and clang.
| + | |
| + | You may install vt via homebrew. |
| | | |
− | == Mac ==
| + | brew tap brewsci/bio |
| + | brew tap brewsci/science |
| + | |
| + | brew install brewsci/bio/vt |
| | | |
− | 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 = |
Line 719: |
Line 723: |
| | | |
| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |
− | #converts in.bcf to tab format with selected INFO fields | + | #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 | + | 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 |
− | CHROM POS REF ALT N_ALLELE EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2 | + | ====== |
− | 20 17548608 A AC 2 2 13 1 1 0 0 17548608 17548608 | + | 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> |
| | | |
− | options : -v print variant CHROM,POS,REF,ALT,N_ALLELE [false] | + | options : -d debug [false] |
− | -d debug [false]
| |
| -f filter expression [] | | -f filter expression [] |
− | -t list of info tags to be extracted [] | + | -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 1,068: |
| 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] | + | 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 1,101: |
| no. of trios : 2 | | no. of trios : 2 |
| no. of variants : 25346 | | no. of variants : 25346 |
− |
| |
− |
| |
| | | |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
Line 1,115: |
Line 1,117: |
| </div> | | </div> |
| </div> | | </div> |
− |
| |
| | | |
| === Profile SNPs === | | === Profile SNPs === |
Line 1,733: |
Line 1,734: |
| = 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]. | + | 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: |
| | | |
Line 1,742: |
Line 1,742: |
| ! scope="col"| Description | | ! scope="col"| Description |
| ! scope="col"| Valid Values | | ! scope="col"| Valid Values |
| + | ! scope="col"| Missing Values |
| |- | | |- |
| |Family ID<br> | | |Family ID<br> |
Line 1,750: |
Line 1,751: |
| Phenotype | | Phenotype |
| |ID of this family <br> | | |ID of this family <br> |
− | ID of this individual <br> | + | 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> |
− | Sex of the individual. <br> | + | Sex of the individual<br> |
− | Phenotype. | + | Phenotype |
− | |[A-Za-z_]+<br> | + | |[A-Za-z0-9_]+<br> |
− | [A-Za-z_]+ <br> | + | [A-Za-z0-9_]+(,[A-Za-z0-9_]+)* <br> |
− | [A-Za-z_]+ <br> | + | [A-Za-z0-9_]+ <br> |
− | [A-Za-z_]+<br> | + | [A-Za-z0-9_]+<br> |
− | 1 = male, 2 = female and other = alternative<br> | + | 1=male, 2=female, other, male, female<br> |
− | [A-Za-z_]+ | + | [A-Za-z0-9_]+ |
| + | | 0 <br> |
| + | cannot be missing <br> |
| + | 0 <br> |
| + | 0 <br> |
| + | other<br> |
| + | -9 |
| |} | | |} |
| | | |
− | Family ID
| + | Examples: |
− | Individual ID
| |
− | Paternal ID
| |
− | Maternal ID
| |
− | Sex (1=male; 2=female; other=unknown)
| |
− | Phenotype
| |
− |
| |
− | | |
− | | |
− | ceu NA12878 NA12891 NA12892 female
| |
− | yri NA19240 NA19239 NA19238 female
| |
| | | |
| + | ceu NA12878 NA12891 NA12892 female -9 |
| + | yri NA19240 NA19239 NA19238 female -9 |
| | | |
− | ceu NA12878,NA12878A 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 0 | + | #allows tools like profile_mendelian to detect duplicates and check for concordance |
− | yri NA19240 NA19239 NA19238 0 | + | ceu NA12878,NA12878A NA12891 NA12892 female case |
| + | yri NA19240 NA19239 NA19238 female control |
| | | |
| + | #allows tools like profile_mendelian to detect duplicates and check for concordance |
| + | ceu NA12412 0 0 female case |
| + | yri NA19650 0 0 female control |
| | | |
| = Resource Bundle = | | = Resource Bundle = |