bcftools filter -e 'TYPE="snp"' input1.vcf -O v -o output1.filter.vcf
bcftools filter -e 'TYPE="snp"' input2.vcf -O v -o output2.filter.vcf
bcftools filter -e 'TYPE="snp"' input3.vcf -O v -o output3.filter.vcf
bcftools filter -e 'TYPE="snp"' input4.vcf -O v -o output4.filter.vcf
bcftools filter -e 'TYPE="snp"' input5.vcf -O v -o output5.filter.vcf

[***@dev1 raw_reads]$ cat parallel.input

input1.vcf
output1.filter.vcf
input2.vcf
output2.filter.vcf
input3.vcf
output3.filter.vcf
input4.vcf
output4.filter.vcf
input5.vcf
output5.filter.vcf

cat parallel.input | parallel -j 3 -k --max-args=2 --joblog parallel.log "bcftools filter -e 'TYPE="snp"' {1} -O v -o {2}"

[filter.c:2278 filters_init1] Error: the tag "snp" is not defined in the VCF header
[filter.c:2278 filters_init1] Error: the tag "snp" is not defined in the VCF header
[filter.c:2278 filters_init1] Error: the tag "snp" is not defined in the VCF header
[filter.c:2278 filters_init1] Error: the tag "snp" is not defined in the VCF header
[filter.c:2278 filters_init1] Error: the tag "snp" is not defined in the VCF header