Question: customize reference genome
0
gravatar for bitpir
3.0 years ago by
bitpir180
bitpir180 wrote:

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 • 766 views
ADD COMMENTlink modified 3.0 years ago by WouterDeCoster44k • written 3.0 years ago by bitpir180
4
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster44k wrote:

Sounds like a job for GATK FastaAlternateReferenceMaker

ADD COMMENTlink written 3.0 years ago by WouterDeCoster44k

Perfect, just what I need. Thanks!

ADD REPLYlink written 3.0 years ago by bitpir180

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by WouterDeCoster44k
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