BAM to G-PhoCS file format conversion
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
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mrnlmishra •
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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).