Retrieving a specific location from reference fasta
I want to retrieve Molecular Location: base pairs 166,259,417 to 166,259,467 on chromosome 2 from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
Requesting you guys to help me out !!!!!!
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mohammedabeddin1 •
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mohammedabeddin1 •
1 answer
Use samtools faidx
samtools faidx file.fasta
samtools faidx file.fasta chr2:166259417-166259467
If you have multiple regions to extract, you can use bedtools getfasta
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Hello mohammedabeddin1!
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