Hi there, I have used gatk to map and build an alternate genome that includes snps from a vcf file. I need to extract given regions from reference (main UCSC human genome) and the alternate genome I produced. Now...I saw I can use biostrings to extract regions from the UCSC reference genome I am using but I can't seem to figure out how to extract those regions from the alternate I produced. e.g. I have region chrY:1234-2345 and I want the two fasta files with these coord from reference and alternate.
I've seen some posts regarding region extraction but they all seem to use only reference genomes and I can't seem to figure out how to get it to work for what I need. Sorry if this has been asked before.
1 answer
How about samtools faidx with -r option: http://www.htslib.org/doc/samtools-faidx.html
You will need to bgzip compress your alternate genome and index it.
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