vembrane uses python expressions to filter variants. From the documentation:

vembrane allows to simultaneously filter variants based on any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the annotation field ANN. When filtering based on ANN, annotation entries are filtered first. If no annotation entry remains, the entire variant is deleted.

References:

• Hartmann, T., Schröder, C., Kuthe, E., Lähnemann, D., and Köster, J. (2022). Insane in the vembrane: filtering and transforming VCF/BCF files. Bioinformatics. PubMed |  PMC |  Journal

• vembrane on GitHub

• Module Name: vembrane (see the modules page for more information)
• Example files in $VEMBRANE_TEST_DATA

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

[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=10g -c2
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 vembrane
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp ${VEMBRANE_TEST_DATA:-none}/HG001* .
[user@cn3144 ~]$ ls -lh
-rw-r--r-- 1 user group  89M Jul  1 13:01 AshkenazimTrio_chr1_annot.bcf
-rw-r--r-- 1 user group 131K Jul  1 13:10 AshkenazimTrio_chr1_annot.bcf.csi
-rw-r--r-- 1 user group  17K Jul  1 12:31 AshkenazimTrio_chr1_annot.vcf_summary.html
[user@cn3144 ~]$ bcf=AshkenazimTrio_chr1_annot.bcf
[user@cn3144 ~]$ ## Count the number of variants marked as HIGH impact per gene in the trio
[user@cn3144 ~]$ vembrane filter -O bcf 'ANN["IMPACT"]=="HIGH"]' $bcf 2> /dev/null \
                    | vembrane table 'ANN["SYMBOL"], ANN["IMPACT"]' \
                    | cut -f1 | sort | uniq -c | sort -k1,1nr | head
     28 PPIEL
     17
     11 FLG-AS1
      8 LINC01360
      7 GCSAML
      6 FCGR2A
      6 FCGR2C
      6 GPATCH4
      6 KIAA0040
      6 KLHDC8A

[user@cn3144 ~]$ vembrane filter -O bcf -o ppiel.bcf 'ANN["SYMBOL"] == "PPIEL"' $bcf 2>/dev/null 
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load vembrane/1.0.5
vembrane filter -O bcf -o output.bcf 'ANN["IMPACT"]=="HIGH"]' input.bcf

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=6g vembrane.sh

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

vembrane filter -O bcf -o output_chr1.bcf 'ANN["IMPACT"]=="HIGH"]' input_chr1.bcf
vembrane filter -O bcf -o output_chr2.bcf 'ANN["IMPACT"]=="HIGH"]' input_chr2.bcf

Submit this job using the swarm command.

swarm -f vembrane.swarm -g 6 -t 2 --module vembrane/1.0.5