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Revision as of 10:37, 10 December 2014
, 10:37, 10 December 2014→Checking if INDEL Completed
How long did INDEL calling take? Look at the log message - time in seconds.
How long did INDEL calling take? Look at the log message - time in seconds.
=== Need a BAM Index File? ===
Check your BAM files
ls $SAMPLE/output/bams/*bam
Check your BAI files
ls $SAMPLE/output/bams/*bai
Do you have the same number of BAM & BAI files?
* If so, then you are good to go.
* If you have more BAI's than BAM's - oops!!! (LET ME KNOW)
* If you have more BAM's than BAI's, we need to generate the index:
*: <pre>$GC/bin/samtools index $SAMPLE/output/bams/YOUR_BAM_WITH_MISSING_BAI.bam</pre>
=== Detach From screen===
Detach from screen. We will resume it again later when we start SNPCall.
Detach from screen. We will resume it again later when we start SNPCall.
Ctrl-a d
Ctrl-a d
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