phASER stands for phasing and Allele Specific Expression from RNA-seq. It performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.

References:

• Castel, Stephane E., et al. "Rare variant phasing and haplotypic expression from RNA sequencing with phASER." Nature communications 7.1 (2016): 1-6.

• phASER on GitHub
• phASER tutorial

• Module Name: phaser (see the modules page for more information)
• phASER has a --threads option. Testing shows that --cpus-per-task should be set to twice the number specified by --threads.
• Example data can be found in /usr/local/apps/phaser/1.1.1/testdata
• Do not preface script calls with python. Just call the phaser*.sh scripts directly and they will use the correct version of Python.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c8 --mem=10g --gres=lscratch:20
salloc.exe: Pending job allocation 63023261
salloc.exe: job 63023261 queued and waiting for resources
salloc.exe: job 63023261 has been allocated resources
salloc.exe: Granted job allocation 63023261
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0873 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn0873 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0873 63023261]$ cp -r /usr/local/apps/phaser/1.1.1/testdata .

[user@cn0873 63023261]$ cd testdata/

[user@cn0873 testdata]$ module load phaser
[+] Loading phaser  1.1.1  on cn0873
[+] Loading singularity  3.6.1  on cn0873

[user@cn0873 testdata]$ phaser.py --vcf NA06986.vcf.gz \
    --bam NA06986.2.M_111215_4.bam --paired_end 1 --mapq 255 --baseq 10 \
    --sample NA06986 --blacklist hg19_hla.bed \
    --haplo_count_blacklist hg19_haplo_count_blacklist.bed --threads 4 \
    --o phaser_test_case

##################################################
              Welcome to phASER v1.1.1
  Author: Stephane Castel (scastel@nygenome.org)
  Updated by: Bishwa K. Giri (bkgiri@uncg.edu)
##################################################

Completed the check of dependencies and input files availability...

STARTED "Read backed phasing and ASE/haplotype analyses" ...
    DATE, TIME : 2020-08-14, 14:14:10
[...snip]
     COMPLETED using 1176416 reads in 481 seconds using 4 threads
     PHASED  23919 of 2142443 all variants (= 0.011164) with at least one other variant
     GENOME WIDE PHASE CORRECTED  1 of 2142443 variants (= 0.000000)
     Global maximum memory usage: 2822.19 (mb)

COMPLETED "Read backed phasing" of sample NA06986 in 00:08:31 hh:mm:ss
DATE, TIME : 2020-08-14, 14:22:42

The End.

[user@cn0873 testdata]$ phaser_gene_ae.py \
    --haplotypic_counts phaser_test_case.haplotypic_counts.txt \
    --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae.txt

##################################################
          Welcome to phASER Gene AE v1.2.0
  Author: Stephane Castel (scastel@nygenome.org)
##################################################

#1 Loading features...
#2 Loading haplotype counts...
sys:1: DtypeWarning: Columns (5,16,17) have mixed types. Specify dtype option on import or set low_memory=False.
#3 Processing results...
    BAM: NA06986.2.M_111215_4
          generating feature level haplotypic counts...
          outputting feature haplotype counts...

[user@cn0873 testdata]$ exit
exit
srun: error: cn0873: task 0: Exited with exit code 130
salloc.exe: Relinquishing job allocation 63023261
salloc.exe: Job allocation 63023261 has been revoked.

[user@biowulf ~]$

Create a batch input file (e.g. phaser.sh). For example:

#!/bin/bash
set -e
module load phaser
phaser.py --vcf NA06986.vcf.gz --bam NA06986.2.M_111215_4.bam --paired_end 1 \
    --mapq 255 --baseq 10  --sample NA06986 --blacklist hg19_hla.bed \
    --haplo_count_blacklist hg19_haplo_count_blacklist.bed --threads 4 \
    --o phaser_test_case

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] phaser.sh

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

phaser_gene_ae.py \
    --haplotypic_counts phaser_test_case.haplotypic_counts1.txt \
    --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae1.txt
phaser_gene_ae.py \
    --haplotypic_counts phaser_test_case.haplotypic_counts2.txt \
    --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae2.txt
phaser_gene_ae.py \
    --haplotypic_counts phaser_test_case.haplotypic_counts3.txt \
    --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae3.txt
phaser_gene_ae.py \
    --haplotypic_counts phaser_test_case.haplotypic_counts4.txt \
    --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae4.txt

Submit this job using the swarm command.

swarm -f phaser.swarm [-g #] [-t #] --module phaser