BAM to G-PhoCS file format conversion
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2.0 years ago
mrnlmishra • 0

Hello,

It will be great if anyone can help me out in converting BAM alignment file to G-PhoCS format that G-PhoCS can take as input.

Thanks, Mrinal

format conversion G-PhoCS BAM alignment • 549 views
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G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome.

You could export reads in the regions you are interested in and then do a multiple sequence alignment with them to be used as input for G-PhoCS (see: convert bam to clustal ) or use this tool that claims to convert a SAM format file to aligned fasta (does not support multiple references).

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