denovoSAVI

In-house python script for identifying de novo germline variants and new homozygous variants from patient-unaffected-parant trio data

Status

Active Development

Usage

• denovoSAVI takes four input files that can be retrieved from the output files of SAVI.

• You will need mother-blood, father-blood, patient-blood, and patient-diseased-specimen bams (if you have) to run SAVI.
  

• All SAVI should have been run with bams in exact order as shown below.
  

• All input files for denovoSAVI listed below should have patient ID in the first column and include all chromosome information.
  

input file 1 - PDfilter results from SAVI (i.e., report.coding.PDfilter.txt) ran with "merged-parant-bam, patient-blood-bam"
input file 2 - PDfilter results from SAVI (i.e., report.coding.PDfilter.txt) ran with "merged-parant-bam, patient-blood-bam, patient-diseased-specimen"
input file 3 - Coding variants from SAVI (i.e., report.coding.txt) ran with "merged-parant-bam, patient-blood-bam, father-bam, mother-bam"
input file 4 - Coding variants from SAVI (i.e., report.coding.txt) ran with "merged-parant-bam, patient-blood-bam, patient-diseased-specimen, father-bam, mother-bam"

• Note that input file 1 and 3 will be from the patients without patient-diseased-specimen data, while input file 2 and 4 are from those with patient-diseased-specimen.
  

When the input files are ready, you can run denovoSAVI by:

python denovosavi.py input1 input2 input3 input4

denovoSAVI will output the number of de novo germline mutations (DNMs) within the cohort as well as a histogram showing the number of DNMs per patient.
It will also create pie charts showing the distribution of variant types.

Contact

For technical questions, contact Yoonhee via email: ynam@connect.ust.hk