Question: Question converting different genetic file formats into another file
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gravatar for john.anderson.ivy
9 weeks ago by
john.anderson.ivy10 wrote:

Hi,

can anyone provde a ppt/pdf/link to a tutorial which can give you detailed information of how to convert any genetic file (BAM, SAM, VCF, FASTQ, FASTA, etc.) in another genetic file format?

I am interested in tools and documentation of how to do this in house. Any expert help would be much appreciated.

Thank you, J

alignment assembly genome • 132 views
ADD COMMENTlink modified 9 weeks ago by Biostar ♦♦ 20 • written 9 weeks ago by john.anderson.ivy10
2

Not all of these files are entirely equivalent, so there are many different ways to convert between files.

For example, BioPython would handle conversions between FASTA/FASTQ/GenBank/GFF and a whole bunch of other formats. For BAM/SAM/FASTQ, you'll be looking for something like samtools.

There isn't really a 'one-stop-shop' for all of these things though, so can you clarify perhaps what your end goal is?

ADD REPLYlink written 9 weeks ago by jrj.healey9.7k
1

To add to jrj.healey's point, there is a difference between data format and information content. Conversion is used to mean any of the transitions including a change in data format, file format and information content. Not all of the above files have similar information content, so you'd end up losing information (or having to add in dummy information) when you go from one format to another.

ADD REPLYlink written 9 weeks ago by RamRS20k
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