bedtools -u not giving unique files

Question

[arya.sagittarius]

The following are the steps Im following: First step to extract sample using bed file is this (here the bedfile is input bedfile converted to Hg38):

tabix -h -R Hg19_to_Hg38_sorted.bed.gz gnomad.genomes.v{g_version}.hgdp_tgp.chr{chr}.vcf.bgz | perl {vcftools} -c {sample_name} > {sample_name}_out.vcf'

output({sample_name}_out.vcf')
chr2    113982416   rs56177103  TATAAAATAAAATAAA    T   .   PASS    .   GT:AAD:DAD:DAF:ADF  0/1:25519,4077:25519,4077:0.13776:0.13776   
chr2    113982416   rs56177103  TATAAAATAAAATAAA    T   .   PASS    .   GT:AAD:DAD:DAF:ADF  0/1:25519,4077:25519,4077:0.13776:0.13776   
chr2    113982416   rs56177103  TATAAAATAAAATAAA    T   .   PASS    .   GT:AAD:DAD:DAF:ADF  0/1:25519,4077:25519,4077:0.13776:0.13776   

as my output file had repeated regions, inorder to extract the unique regions im using the same input bed file with intersect bed , but unable to get the unique reads. It gives the same repeated results. why is that so ? The following is the cmd that I had used:

bedtools/intersectBed -u -a  {sample_name}_out.vcf' -b bed_filename > output.vcf 

[arya.sagittarius]

Was also wondering if doing sort|uniq gives the same result?

Answer 1

[Alex Reynolds]

Another option is to pipe BED data to sort-bed:

$ ... | sort-bed --unique - > answer.bed

Ref.: https://bedops.readthedocs.io/en/latest/content/reference/file-management/sorting/sort-bed.html

[arya.sagittarius]

But one of my data is a vcf file