From the documentation:

Improved variant filtering and polishing via k-mer validation

References:

• G. Formenti et al. Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nature Methods 2022. PubMed |  PMC |  Journal

• merfin on GitHub
• Best practices

• Module Name: merfin (see the modules page for more information)
• merfin is multithreaded. Match the number of allocated CPUs to the number of threads
• Example files in $MERFIN_TEST_DATA

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

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=36g --gres=lscratch:100
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/$SLURM_JOB_ID
[user@cn3144]$ module load merfin
[user@cn3144]$ # unpack a meryl k-mer database created from PE 250pb illumina reads from the son of a trio
[user@cn3144]$ # with     meryl count k=21 reads.fastq.gz output HG002.k21.meryl
[user@cn3144]$ # followed by excluding kmers with frequency of 1
[user@cn3144]$ tar -xzf ${MERFIN_TEST_DATA:-none}/HG002.k21.gt1.meryl.tar.gz
[user@cn3144]$ cp ${MERFIN_TEST_DATA:-none}/{chr20.fasta.gz,ill.vcf.gz} .
[user@cn3144]$ merfin -filter -sequence chr20.fasta.gz  \
           -memory 34 \
           -threads $SLURM_CPUS_PER_TASK \
           -readmers HG002.k21.gt1.meryl \
           -vcf ill.vcf.gz               \
           -output test.merfin

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

Create a batch input file (e.g. merfin.sh), which uses the input file 'merfin.in'. For example:

#!/bin/bash
module load merfin
tar -xzf ${MERFIN_TEST_DATA:-none}/HG002.k21.gt1.meryl.tar.gz
cp ${MERFIN_TEST_DATA:-none}/{chr20.fasta.gz,ill.vcf.gz} .
merfin -filter -sequence chr20.fasta.gz  \
    -memory 34 \
    -threads $SLURM_CPUS_PER_TASK \
    -readmers HG002.k21.gt1.meryl \
    -vcf ill.vcf.gz               \
    -output test.merfin

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=36g merfin.sh