bedtools
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arq5x
A powerful toolset for genome arithmetic.
Most of the time that I want to use subtractBed, the b file is very big (e.g.: 2 GiB: 66 million lines) as it contains all known snp positions. This...
Hi Aaron - I have some VCF files with a blank line after the `#CHROM...` header line. BEDTools programs operating on these VCFs only report 2 columns (chrom, pos) rather...
bedtools apparently throws an error when trying to read empty files, and treats them as though they cannot be opened. When I try to intersect 2 blank files, this is...
What steps will reproduce the problem? 1. windowBed -a file1.bed -b file2.bed -c f 1.0 What is the expected output? What do you see instead? I expect counts of the...
The significance testing used by ENCODE as developed by Bickel et al (http://arxiv.org/pdf/1101.0947.pdf) and available here: http://www.encodestatistics.org/ (IIUC) seems to rely on shuffling within prescribed regions. Part of their method...
This would be useful for stuff related to significance of overlap (along with shuffle). this would have a command-line interface like: ``` bedtools sample -i stdin -n 500 > out.500.bed...
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Hi, I run the genomecov using the commond line as below: $ bedtools genomecov -ibam Pp-BWAmemNCBI-90Grmdupl.bam -d > coverage.log The input bam was generation by using BWA-mem for mapping, picard...
