Question

customize reference genome

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6.8 years ago

bitpir ▴ 240

How do you customize a reference genome, say, hg19, and make into a personalized reference genome in fasta format? I don't have the phased sequence information, but I have the fastq's, bam, and vcf formats.

DNA-seq • 1.6k views

ADD COMMENT • link updated 6.8 years ago by WouterDeCoster 47k • written 6.8 years ago by bitpir ▴ 240

score 4 · Accepted Answer · 2017-07-06

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6.8 years ago

WouterDeCoster 47k

Sounds like a job for GATK FastaAlternateReferenceMaker

ADD COMMENT • link 6.8 years ago by WouterDeCoster 47k

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Perfect, just what I need. Thanks!

ADD REPLY • link 6.8 years ago by bitpir ▴ 240

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Glad to help. If my answer resolved your question you should accept it to mark this question as solved. Upvote|Bookmark|Accept

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k