Input: BAM files (tested for up to 50,000) from short read paired end whole genome sequencing data

Output: Called deletions in VCF file

Note: The default reference genome is GRCh38 (Genome Reference Consortium Human Build 38). For other reference genomes, human or other diploid organism, it is necessary to specify user-defined sampling intervals. See Sampling intervals for parameter estimation.

For more detailed information see the Wiki.

git clone https://github.com/kehrlab/PopDel.git
cd PopDel
sudo make install

or with conda:

conda install -c bioconda popdel

Note: PopDel takes significantly more time for calling variants when installed via conda.

Create insert size profiles for each individual sample

# Create a profile for each BAM-file
popdel profile myBam1.bam
popdel profile myBam2.bam
popdel profile myBamN.bam

For more options see Wiki: PopDel Profile

Joint calling on list of all profiles

# Create a list of all profiles
realpath myBam*.profile > myProfiles.txt
# Run calling on all profiles
popdel call myProfiles.txt

For more options see Wiki: PopDel Call

See wiki for more information on how to view the profile with PopDel View and interpret the output in VCF-format.

Sebastian Roskosch, Hákon Jónsson, Eythór Björnsson, Doruk Beyter, Hannes P. Eggertsson, Patrick Sulem, Kári Stefánsson, Bjarni V. Halldórsson, Birte Kehr.
PopDel identifies medium-size deletions jointly in tens of thousands of genomes. Submitted for publication
Preprint available at bioRxiv 740225; doi: https://doi.org/10.1101/740225

    Last update: 2019-08-30
    PopDel version: 1.1.2
    SeqAn version: 2.3.1 (modified)
    Author: Sebastian Roskosch (Sebastian.Roskosch[at]bihealth.de)

PopDel is distributed under the GPL-3.0. Consult the accompanying LICENSE file for more details.