WHATSHAP on Biowulf
WhatsHap is an application for phasing genomic variants using DNA sequencing reads.
References:
- WhatsHap: fast and accurate read-based phasing. Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O. Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schoenhuth, Tobias Marschall. bioRxiv 085050
- WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth. Journal of Computational Biology, 22(6), pp. 498-509, 2015.
Documentation
Important Notes
- Module Name: whatshap (see the modules page for more information)
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 input in bold):
[user@biowulf]$ sinteractive 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 whatshap [user@cn3144 ~]$ cd /data/$USER/WHATSHAP_TEST [user@cn3144 ~]$ whatshap phase -o phased.vcf input.vcf pacbio_reads_30x.bam Working on 1 samples from 1 family ======== Working on chromosome 'contig1' ---- Processing individual SAMPLE Using maximum coverage per sample of 15X Number of variants skipped due to missing genotypes: 0 Number of remaining heterozygous variants: 177 Reading alignments for sample 'SAMPLE'and detecting alleles ... WARNING: Sample 'SAMPLE' not found in any BAM/CRAM file. Found 0 reads covering 0 variants Kept 0 reads that cover at least two variants each Reducing coverage to at most 15X by selecting most informative reads ... Selected 0 reads covering 0 variants Best-case phasing would result in 0 non-singleton phased blocks (0 in total) ... after read selection: 0 non-singleton phased blocks (0 in total) Variants covered by at least one phase-informative read in at least one individual after read selection: 0 Phasing 1 sample by solving the MEC problem ... MEC cost: 0 No. of phased blocks: 0 ======== Writing VCF Done writing VCF ======== Working on chromosome 'contig2' ---- Processing individual SAMPLE Using maximum coverage per sample of 15X Number of variants skipped due to missing genotypes: 0 Number of remaining heterozygous variants: 134 Reading alignments for sample 'SAMPLE'and detecting alleles ... WARNING: Sample 'SAMPLE' not found in any BAM/CRAM file. Found 0 reads covering 0 variants Kept 0 reads that cover at least two variants each Reducing coverage to at most 15X by selecting most informative reads ... Selected 0 reads covering 0 variants Best-case phasing would result in 0 non-singleton phased blocks (0 in total) ... after read selection: 0 non-singleton phased blocks (0 in total) Variants covered by at least one phase-informative read in at least one individual after read selection: 0 Phasing 1 sample by solving the MEC problem ... MEC cost: 0 No. of phased blocks: 0 ======== Writing VCF Done writing VCF ======== Working on chromosome 'contig3' ---- Processing individual SAMPLE Using maximum coverage per sample of 15X Number of variants skipped due to missing genotypes: 0 Number of remaining heterozygous variants: 165 Reading alignments for sample 'SAMPLE'and detecting alleles ... WARNING: Sample 'SAMPLE' not found in any BAM/CRAM file. Found 0 reads covering 0 variants Kept 0 reads that cover at least two variants each Reducing coverage to at most 15X by selecting most informative reads ... Selected 0 reads covering 0 variants Best-case phasing would result in 0 non-singleton phased blocks (0 in total) ... after read selection: 0 non-singleton phased blocks (0 in total) Variants covered by at least one phase-informative read in at least one individual after read selection: 0 Phasing 1 sample by solving the MEC problem ... MEC cost: 0 No. of phased blocks: 0 ======== Writing VCF Done writing VCF == SUMMARY == Maximum memory usage: 0.050 GB Time spent reading BAM/CRAM: 0.0 s Time spent parsing VCF: 0.1 s Time spent selecting reads: 0.0 s Time spent phasing: 0.0 s Time spent writing VCF: 0.1 s Time spent finding components: 0.0 s Time spent on rest: 0.0 s Total elapsed time: 0.2 s [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. whatshap.sh). For example:
#!/bin/bash
set -e
module load whatshap
whatshap phase -o /data/$USER/WHATSHAP_TEST/phased.vcf \
/data/$USER/WHATSHAP_TEST/input.vcf \
/data/$USER/WHATSHAP_TEST/pacbio_reads_30x.bam
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] whatshap.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. whatshap.swarm). For example:
whatshap phase -o /data/$USER/WHATSHAP_TEST/phased_A.vcf \
/data/$USER/WHATSHAP_TEST/input_A.vcf \
/data/$USER/WHATSHAP_TEST/pacbio_reads_A.bam
whatshap phase -o /data/$USER/WHATSHAP_TEST/phased_B.vcf \
/data/$USER/WHATSHAP_TEST/input_B.vcf \
/data/$USER/WHATSHAP_TEST/pacbio_reads_B.bam
Submit this job using the swarm command.
swarm -f whatshap.swarm [-g #] [-t #] --module whatshapwhere
| -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 whatshap | Loads the whatshap module for each subjob in the swarm |