How To Convert Eland File To Bam?

Question

[Zack]

Does anyone know if it is possible to convert Eland file to BAM?

[Biomed]

There is no such thing as an ELAND file. There are files created by ELAND or ELAND2. What is the extension of the file? is it a fastq file is it an export file? are there more than one files? Is this from a paired end or a single end sequencing project?

Answer 1

[Ian]

Samtools http://samtools.sourceforge.net/ includes a script called export2sam.pl. I have not used it myself, but its use is mentioned here: http://genomewiki.ucsc.edu/index.php/ABRF2010_Tutorial, under 'Viewing alignments in BAM format'.

You would then use: samtools view -bS -o out.bam in.sam