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Preserve Case when Using FastaAlternateReferenceMaker

nathanhaighnathanhaigh Adelaide, AustraliaMember

I had soft masked a FASTA file using BEDTools' maskfasta and wanted to use this as input to FastaAlternateReferenceMaker as well as a VCF file. I was suprised to see that FastaAlternateReferenceMaker had undone all the soft masking and output all uppercase bases. I would like to be able to preserve the case of my input reference sequence.

My particular use case is as follows:
1) I had performed a read mapping against a reference genome
2) I called variants from this mapping to create a VCF
3) I soft masked bases which had zero coverage from my reads
4) I wanted to use the soft masked reference plus VCF to generate a new reference for my sample where the output would still contain the information about which bases had zero coverage from my sample.

Issue · Github
by Geraldine_VdAuwera

Issue Number
Last Updated


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @nathanhaigh,

    Our reference utilities are a bit primitive because we don't use them much ourselves -- the lack of case sensitivity was no doubt an oversight. So we'll put in a feature request to get this done, though I can't guarantee when we'll get to it.

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