https://github.com/ryanlayer/svv

Stupid Simple Structural Variant View
https://github.com/ryanlayer/svv

Last synced: 4 months ago
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Stupid Simple Structural Variant View

• Host: GitHub
• URL: https://github.com/ryanlayer/svv
• Owner: ryanlayer
• Created: 2016-02-01T21:46:03.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-11-21T19:43:45.000Z (over 7 years ago)
• Last Synced: 2024-01-17T00:57:31.881Z (6 months ago)
• Language: Python
• Homepage:
• Size: 15.2 MB
• Stars: 25
• Watchers: 3
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

Lists

• awesome-genome-visualization - svv
• repo-5916-awesome-genome-visualization - svv - genome-visualization/svv.png) (Static)

README

        
# Stupid Simple Structural Variant View

A two-step process that can help visualize the coverage near a variant across multiple BAMs.

Step 1: Create a coverage file for each variant in a VCF.  (NOTE: use [GQT](https://github.com/ryanlayer/gqt), [bcftools](https://github.com/samtools/bcftools), [bedtools](https://github.com/arq5x/bedtools2) etc to filter your full VCF down to a more interesting/managable subset.)

    $ bcftools view test/test.vcf.gz | ./sv_depth.py test/test.ped 1000

    

`sv_depth.py` creates a covrage file  "var_ID.txt" for each SV in the VCF, where ID is the variant ID (3rd column of the variant record).  In this case, `test/test.vcf.gz` has two variants, `DEL_pindel_18715` and  `UW_VH_5456`, and so it creates `var_DEL_pindel_18715.txt` and `var_UW_VH_5456.txt`.  The two parameters to `sv_depth.py` are the ped file (where the 8th column is a path to the BAM files) and a the distance up and down stream of the the SV that is inclued in the coverage file.

Step 2: Visualize these coverages with `spark.py`, which takes an exome file, a map from transcrip to gene name, and an ouputfile.

  

    $ cat var_DEL_pindel_18715.txt \

        | ./spark.py \

            -e data/h37_ensemble_exons.bed.gz \

            -n data/h37_ensemble_exons.togenename.txt \

            -o var_DEL_pindel_18715.png

![var_DEL_pindel_18715.png](test/var_DEL_pindel_18715.png)

    $ cat var_UW_VH_5456.txt \

        | ./spark.py \

            -e data/h37_ensemble_exons.bed.gz \

            -n data/h37_ensemble_exons.togenename.txt \

            -o var_UW_VH_5456.png

![var_UW_VH_5456.png](test/var_UW_VH_5456.png)