PopDel - Population-wide Deletion Calling

Input: BAM/CRAM 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). Other human reference builds can be specified in the options. See Specifying the reference genome. For other diploid organism or custom reference builds, it is necessary to specify user-defined sampling intervals. See Sampling intervals for parameter estimation.

Quickstart

For more detailed information see the Wiki.

Installation

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.

Step 1: Create profile

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

Step 2: Call deletions

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.

Citation

Sebastian Niehus, Hákon Jónsson, Janina Schönberger, Eythór Björnsson, Doruk Beyter, Hannes P. Eggertsson, Patrick Sulem, Kári Stefánsson, Bjarni V. Halldórsson, Birte Kehr. PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes. Nat Commun 12, 730 (2021). https://doi.org/10.1038/s41467-020-20850-5

Version and License

    Last update: 2021-03-25
    PopDel version: 1.5.0
    SeqAn version: 2.1 (with HTSlib support added by Hannes P.Eggertsson)
    Author: Sebastian Niehus (Sebastian.Niehus[at]ukr.de)

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