0-indexed or 1-indexed for the SNP output?

FelixKrueger / SNPsplit

Allele-specific alignment sorting

http://felixkrueger.github.io/SNPsplit/

GNU General Public License v3.0

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0-indexed or 1-indexed for the SNP output? #60

Closed sshen82 closed 2 years ago

sshen82 commented 2 years ago

Hi, Thank you for this excellent software! I have a small question about the SNPsplit_genome_preparation output. For example, for a SNP as below, does this correspond to the second or the third letter in chromosome 9?

SNP-ID Chromosome Position Strand Ref/SNP 1 9 2 1 T/G

FelixKrueger commented 2 years ago

I suppose the position will be carried through from the VCF file. As the VCF file of the Mouse Genomes Project is Ensembl-based, I would guess that the default would be 1-based coordinates.

sshen82 commented 2 years ago

Get it. Thank you for your help!