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Revision as of 09:41, 11 July 2014
, 09:41, 11 July 2014→GotCloud BAM Index File
We need to add these BAMs to our index
We need to add these BAMs to our index
* Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline
* Append the bam.index from the pre-aligned BAMs to the one you generated from the alignment pipeline
** '''Be sure to do this command just once'''
cat ${SS}/bams/bam.index >> ${OUT}/bam.index
cat ${SS}/bams/bam.index >> ${OUT}/bam.index
* ">>" will append to the file that follows it
* ">>" will append to the file that follows it
** Check that your BAM index is the correct size
** Check that your BAM index is the correct size
**:<pre>wc -l ${OUT}/bam.index</pre>
**:<pre>wc -l ${OUT}/bam.index</pre>
