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| === Profile SNPs === | | === Profile SNPs === |
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− | 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> |
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| === Profile Indels === | | === Profile Indels === |