Short tandem repeats (STRs) are highly repetitive genomic sequences comprised of repeated copies of an underlying motif. Prevalent in most organisms' genomes, STRs are of particular interest because they mutate much more rapidly than most other genomic elements. As a result, they're extremely informative for genomic identification, ancestry inference and genealogy. Despite their utility, STRs are particularly difficult to genotype. The repetitive sequence responsible for their high mutability also results in frequent alignment errors that can complicate and bias downstream analyses. In addition, PCR stutter errors often result in reads that contain additional or fewer repeat copies than the true underlying genotype.

HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by:

• Learning locus-specific PCR stutter models using an EM algorithm
• Mining candidate STR alleles from population-scale sequencing data
• Employing a specialized hidden Markov model to align reads to candidate alleles while accounting for STR artifacts
• Utilizing phased SNP haplotypes to genotype and phase STRs

References:

https://www.nature.com/articles/nmeth.4267

• https://github.com/tfwillems/HipSTR

• Module Name: hipstr (see the modules page for more information)
• HipSTR is easy to run: HipSTR -h
• Example files can be copied from: /usr/local/apps/hipstr/HipSTR-tutorial

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

[user@biowulf]$ sinteractive --mem=4g
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]$ module load hipstr
[user@cn3144]$ cp -r /usr/local/apps/hipstr/HipSTR-tutorial /data/$USER; cd /data/$USER/HipSTR-tutorial
[user@cn3144]$ export bam=/data/$USER/HipSTR-tutorial/bams
[user@cn3144]$ export fasta=/data/$USER/HipSTR-tutorial/fasta
[user@cn3144]$ export tut=/data/$USER/HipSTR-tutorial
[user@cn3144]$ HipSTR --bams $bam/ERR194147.bam,$bam/ERR194160.bam,\
                                $bam/ERR194161.bam,$bam/SRR826427.bam,\
                                $bam/SRR826428.bam,$bam/SRR826448.bam,\
                                $bam/SRR826463.bam,$bam/SRR826465.bam,\
                                $bam/SRR826467.bam,$bam/SRR826469.bam,\
                                $bam/SRR826471.bam,$bam/SRR826473.bam \
                        --fasta $fasta/all_chroms.fa \
                        --regions $tut/regions.bed \
                        --str-vcf $tut/trio.marshfield.vcf.gz \
                        --log $tut/trio.marshfield.log \
                        --viz-out $tut/trio.marshfield.viz.gz \
                        --min-reads 25 --def-stutter-model

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

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

#!/bin/bash
#SBATCH --job-name=hipstr
#SBATCH --output=hipstr.out
#SBATCH --ntasks=1
#SBATCH --mem=4g
#SBATCH --time=30:00
#SBATCH --partition=quick

set -e
module load hipstr
cp -r /usr/local/apps/hipstr/HipSTR-tutorial /data/$USER
cd /data/$USER/HipSTR-tutorial
HipSTR --bams $bam/ERR194147.bam,$bam/ERR194160.bam,\
              $bam/ERR194161.bam,$bam/SRR826427.bam,\
              $bam/SRR826428.bam,$bam/SRR826448.bam,\
              $bam/SRR826463.bam,$bam/SRR826465.bam,\
              $bam/SRR826467.bam,$bam/SRR826469.bam,\
              $bam/SRR826471.bam,$bam/SRR826473.bam \
        --fasta $fasta/all_chroms.fa \
        --regions $tut/regions.bed \
        --str-vcf $tut/trio.marshfield.vcf.gz \
        --log $tut/trio.marshfield.log \
        --viz-out $tut/trio.marshfield.viz.gz \
        --min-reads 25 --def-stutter-model

Submit the job:

sbatch hipstr.sh

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

cd dir1;HipSTR ....... --def-stutter-model
cd dir2;HipSTR ....... --def-stutter-model
cd dir3;HipSTR ....... --def-stutter-model

Submit this job using the swarm command.

swarm -f hipstr.swarm -g 8 --module hipstr