From Genome Analysis Wiki
Jump to navigationJump to search
2 bytes added
, 14:40, 14 February 2016
Line 1,050: |
Line 1,050: |
| <div class=" mw-collapsible mw-collapsed"> | | <div class=" mw-collapsible mw-collapsed"> |
| | | |
− | vt profile_vntrs vntrs.sites.bcf -g vntr.reference.txt
| + | #profiles a set of VNTRs |
| + | vt profile_vntrs vntrs.sites.bcf -g vntr.reference.txt |
| | | |
| + | |
| profile_vntrs v0.5 | | profile_vntrs v0.5 |
| | | |
Line 1,092: |
Line 1,094: |
| # 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 coding VNTRs. |
| # 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. |
Line 1,104: |
Line 1,106: |
| | | |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | usage : vt profile_indels [options] <in.vcf> | + | usage : vt profile_vntrs [options] <in.vcf> |
| | | |
| options : -g file containing list of reference datasets [] | | options : -g file containing list of reference datasets [] |