keeping heterozygote information in fasta format from .bam files
Hi everyone,
I’m using the GATK “FastaAlternateReferenceMaker” walker to pull out candidate gene sequences from my .bam files. What I would like to do is create alignments of particular genes across multiple individuals, then assess the sequence and SNP for evidence of selection (Dn / Ds ratios etc). My problem is that FastaAlternateReferenceMaker squashes out heterozygous positions to include only the consensus base. Given it is designed to make a ‘reference’ sequence this is understandable.
I can’t see a way to direct FastaAlternateReferenceMaker to keep the heterozygote information by incorporating IUPAC nucleotides (C/T = Y etc). Do you know of an alternative tool I can use that will do this? Any help appreciated!
Cheers
I’m using the GATK “FastaAlternateReferenceMaker” walker to pull out candidate gene sequences from my .bam files. What I would like to do is create alignments of particular genes across multiple individuals, then assess the sequence and SNP for evidence of selection (Dn / Ds ratios etc). My problem is that FastaAlternateReferenceMaker squashes out heterozygous positions to include only the consensus base. Given it is designed to make a ‘reference’ sequence this is understandable.
I can’t see a way to direct FastaAlternateReferenceMaker to keep the heterozygote information by incorporating IUPAC nucleotides (C/T = Y etc). Do you know of an alternative tool I can use that will do this? Any help appreciated!
Cheers
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