bedtools -u not giving unique files

Question

[arya.sagittarius]

The following are the steps I'm 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, to extract the unique regions I'm using the same input bed file with intersect bed, but I'm 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