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Extract Alu Repeats

Hello. I have snp data (vcf files) and would like to extract those events that happen on Alu repeats from those that don't. Reading the threads here in BIOSTAR, I gather that potential options to do this are the tools RepeatMasker, TANTAN and TRF. I also read that each of these has its drawbacks. Can somebody advice on the tool that works best for this purpose? Thanks, G

repeats
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updated by Kanhu charan Moharana • Kanhu charan Moharana • written by GPR GPR

2 answers

You can download RepeatMasker tracks in BED format from UCSC's Table Browser. Choose your genome of interest, and get the data with the settings:

  • group: Variation and Repeats
  • track: RepeatMasker
  • table: rmsk
  • output format: BED

Assuming you save the results as output.bed, you can then grep out the Alu regions of interest and intersect with BEDTools:

grep "Alu" output.bed > alu.bed
bedtools intersect -a mydata.vcf -b alu.bed > snps-in-alu.vcf
bedtools intersect -a mydata.vcf -b alu.bed -v > snps-not-in-alu.vcf
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written by Ryan Dale Ryan Dale

thanks so much! I will try this.

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written by GPR GPR

Am trying to get the same results, thus, am trying to get the ALU coordinates for the human chromosome 1. I tried to follow as you suggested but 1) thhere is no possibility of choosing Variations and Repeat, just one option can be selected and 2) once i selected Repeat i get "No results for that query".... can somebody help me pls.....

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written by ojeillo • ojeillo

I ve used bedtools intersect approach using VCF file, but it gives an error: Error: malformed BED entry at line 2. Start was greater than end. Exiting.

So I converted vcf file to bed format and it worked fine for me. 

awk '{print $1"\t"$2"\t"$2}' 1233_variant_pos_final.vcf >1233_variant_pos_final.bed

Also better to sort all the input the bed files.

sort -k 1,1 -k2,2n hg19_Alu.bed > hg19_Alu_sorted.bed
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written by Kanhu charan Moharana • Kanhu charan Moharana

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