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I have the CDS sequences for my genome. I want to align Illumina DNA seq reads from related fungal strains to these. This is to identify SNPs in just the coding sequences. I am not sure if I should use a DNA seq aligner like BWA and Bowtie, or to use a split aware aligner like STAR.

I have the full genome. But I wanted the SNPs for each of the CDS sequences, so I can create consensus sequences for these CDS for the related strains.

Can you provide examples or links to get alignment from CDS region or using VCFtools to get SNPs and INDELs from the CDS region? I have tried looking but haven't found anything useful. Thank you.

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Answer from @fabio-marroni, converted from comment:

I suggest that you align to the full genome and after this, you only extract the SNPs in the CDS. This procedure is commonly used in all exome sequencing projects, so you can find a lot of instructions software. You can choose between extracting the regions from the alignment (using samtools), or keeping everything, calling the SNPs and then only select those in CDS using vcftools.

For looking at the CDS region, you could try bedtools, as suggested here.

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