BAM to G-PhoCS file format conversion

Question

[mrnlmishra]

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

[GenoMax]

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).