Question: What happens to heterozygous sites when you go from reference sequence to sequence modified by variants?
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gravatar for jxiang15
4.1 years ago by
jxiang1510
United States
jxiang1510 wrote:

In a previous post, New Fasta Sequence From Reference Fasta And Variant Calls File?, it was recommended to use either vcftools or FastaAlternateReferenceMaker (https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php)  if you have a reference sequence and a variant file, and you to get a new FASTA file. 

However, with the 1000 genomes data, the data is phased.  So at heterozygous sites, should the ALT allele be substituted or should the REF allele be left in the sequence? 

Thanks in advance

snp sequence • 1.4k views
ADD COMMENTlink modified 4.1 years ago by geek_y9.1k • written 4.1 years ago by jxiang1510
0
gravatar for geek_y
4.1 years ago by
geek_y9.1k
Barcelona/CRG/London/Imperial
geek_y9.1k wrote:

FastaAlternateReferenceMaker's --useIUPAC option will place the IUPAC code wherever there is heterozygous state.

ADD COMMENTlink written 4.1 years ago by geek_y9.1k

What happens if you don't put that option, what is the default behaviour?

ADD REPLYlink written 4.1 years ago by jxiang1510
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