Mutations Investigation

BioSeq Group, Tufts University

BioSeq Program Administrator: Matt Fierman (bioseq@tufts.edu)

Author: Mark Hartman (markrhartman@gmail.com)

Introduction

This analysis pipeline analyses the VCF results from the Mutations Investigation Experiment from the Illumina MiSeq. Currently consists of a single tiny script.

Setup

Put all of the VCF files generated by the MiSeq in the same directory as the script. The script uses all files in this folder that have the ".vcf" file extension, so make sure there are no other files of this type in the same folder.

Use

./combineVCFs.py (very simple)

Output

For each run, the combineVCFs.py script creates tab-separated text file "combinedVCFs.txt" in the following format. Example: AB2_S9 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AB2 pUC19 3 . G C 177.01 PASS AC=1;AF=0.5;AN=2;DP=41;QD=4.32 GT:AD:DP:GQ:PL:VF:GQX 0/1:25,16:41:99:207,0,480:0.390:99 pUC19 16 . A C 77.01 PASS AC=1;AF=0.5;AN=2;DP=229;QD=0.34 GT:AD:DP:GQ:PL:VF:GQX 0/1:182,47:238:99:107,0,4243:0.205:77 pUC19 1631 . A G 112964.01 PASS AC=2;AF=1.0;AN=2;DP=3260;QD=34.65 GT:AD:DP:GQ:PL:VF:GQX 1/1:4,3256:3264:99:112964,8378,0:0.999:99 pUC19 2680 . C G 25.02 PASS AC=1;AF=0.5;AN=2;DP=207;QD=0.12 GT:AD:DP:GQ:PL:VF:GQX 0/1:162,45:209:54.85:55,0,2384:0.217:25

Further Analysis

Once the VCF files are combined into a single file, this file can be formatted into a summary sheet for exploring the various mutations identified in the run.

Questions? Comments? Suggestions? Don't hesitate to contact us!