🤖Detecting Tandem Repeats Across Genome

Detecting whole-genome TR using a pre-defined bed file would take a long time. We took about 60 hours on 25 threads.

#Download at: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/
#simpleRepeat.txt.gz
gunzip simpleRepeat.txt.gz
#turn the txt into bed file
grep -v '^#' simpleRepeat.txt | awk -vOFS='\t' 'length($17)>1 {print $2,$3,$4,$17,$5,$5}' > simple_repeats.bed
#spliting the bed would save much time when only interested in certain region. Here's a simplest example
split -l 10000 -d -a 4 --additional-suffix=.bed simple_repeats.bed batch

Here's an actual case after detection based on one splited bed.

1MB

batch000_TR.vcf