This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bedtools -u not giving unique files

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
bedtools intersectbed vcftools vcf tabix
• 1,503 views • link
updated by Ram Ram • written by arya.sagittarius • arya.sagittarius

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

• 0 views • link
written by arya.sagittarius • arya.sagittarius

1 answer

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

• 0 views • link
written by Alex Reynolds Alex Reynolds

Log in to answer this question.

More posts like this