Questions tagged [bedtools]

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-9
votes
1answer
290 views

Extracting the number SNP in each range

I have called copy number and I have 2 files (I have shared the link of my files ); One contains some ranges ...
7
votes
5answers
2k views

Merging bed records based on name

I generated a file starting with the following bed lines: ...
4
votes
2answers
154 views

Using column 2 of one file to match with two columns of another file, and append

I have file 1 like following: 1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 16855676 16855696 CTGTCCAGCAGAGGGCGGTG And file 2 as following ...
1
vote
3answers
120 views

Masking sites in a vcf file

I need to mask all sites in a vcf file flagged by the 1000 Genomes Project as being unfit for population genetic analyses. The sites for all chromosomes are available at: 1000Genomes masked sites From ...