How to use SNPsplit in galaxy on mouse genome bam files to allign to two different mouse strains or is there anyother alternative...i need the output in .bam format

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How can we do SNPsplit in galaxy on Mouse genome aligned bam files? I have to align to two different mouse strains

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Hi @Isha_Singh
do you mean SNPsplit available on Galaxy Australia or something else? SNPsplit does not work on BAM files. According to the description, the input and output are tabular files.
Can you provide more info?
Thank you!
Igor

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Hello Igor,
Thanks for your interest.
I am talking about allele specific alignment of sequencing reads. It’s done by SNPsplit( * DOI: 10.12688/f1000research.9037.2), tool by Felix Krueger and Simon R Andrews.
I have to read files my BAM files and determine the allelic origin of reads using known single nucleotide polymorphic (SNP) for two different mouse strains C57bl/6 and DBA2J.
I am unable to find anything for the same in Galaxy.
Any suggestion would be a great help.
Thanks again,

Isha

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Hi Isha,

I don’t see SNPsplit in the main Galaxy tool shed, so it seems the tool is not available for Galaxy platform.
Maybe someone else can comment on available alternatives.
Kind regards,
Igor