Biowulf High Performance Computing at the NIH
peddy on Biowulf

peddy is used to compare sex and familial relationships given in a PED file with those inferred from a VCF file. This is done by sampling 25000 sites plus chrX from the VCF file to estimate relatedness, heterozygosity, sex and ancestry. It uses data from the thousand genome project.

References:

  • Brent S. Pedersen, Aaron R. Quinlan. Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. Am. J. Hum. Genetics 2017, 3:406-413. PubMed |  PMC |  Journal
Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=2 --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp -r $PEDDY_TEST_DATA/data .
[user@cn3144]$ peddy -p $SLURM_CPUS_PER_TASK --plot --prefix ceph-1463 \
                     data/ceph1463.peddy.vcf.gz data/ceph1463.ped
2018-05-21 08:14:22 cn4242 peddy.cli[35381] INFO Running Peddy version 0.3.1
2018-05-21 08:14:23 cn4242 peddy.cli[35381] INFO ped_check
[...snip...]
[user@cn3144]$ ls -lh
-rw-r--r-- 1 user group 169K May 21 08:14 ceph-1463.background_pca.json
-rw-r--r-- 1 user group 2.0K May 21 08:14 ceph-1463.het_check.csv
-rw-r--r-- 1 user group  18K May 21 08:14 ceph-1463.het_check.png
-rw-r--r-- 1 user group 211K May 21 08:14 ceph-1463.html
-rw-r--r-- 1 user group 118K May 21 08:14 ceph-1463.pca_check.png
-rw-r--r-- 1 user group  13K May 21 08:14 ceph-1463.ped_check.csv
-rw-r--r-- 1 user group 108K May 21 08:14 ceph-1463.ped_check.png
-rw-r--r-- 1 user group   96 May 21 08:14 ceph-1463.ped_check.rel-difference.csv
-rw-r--r-- 1 user group 1.7K May 21 08:14 ceph-1463.peddy.ped
-rw-r--r-- 1 user group  835 May 21 08:14 ceph-1463.sex_check.csv
-rw-r--r-- 1 user group  25K May 21 08:14 ceph-1463.sex_check.png

[user@cn3144]$

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

peddy creates several plots, data tables, and a sumamry report in html. This includes, for example, the following check on ancestry showing reported ancestry in the pedigree overlayed on a PCA of background genomes.

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. peddy.sh), which uses the data in $PEDDY_TEST_DATA. For example:

#! /bin/bash
# this file is peddy.batch
module load peddy/0.2.9 || exit 1

td=/usr/local/apps/peddy/TEST_DATA/data
cp -r $PEDDY_TEST_DATA/data .
peddy -p $SLURM_CPUS_PER_TASK --plot --prefix ceph-1463 \
    data/ceph1463.peddy.vcf.gz data/ceph1463.ped

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=4g peddy.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. peddy.swarm). For example:

peddy -p $SLURM_CPUS_PER_TASK --plot --prefix fam1 fam1/fam1.vcf.gz fam1/fam1.ped
peddy -p $SLURM_CPUS_PER_TASK --plot --prefix fam2 fam2/fam2.vcf.gz fam2/fam2.ped
peddy -p $SLURM_CPUS_PER_TASK --plot --prefix fam3 fam3/fam3.vcf.gz fam3/fam3.ped

Submit this job using the swarm command.

swarm -f peddy.swarm -g 4 -t 4 --module peddy/0.2.9
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module peddy Loads the peddy module for each subjob in the swarm