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, 22:12, 18 May 2015
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| 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. |
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− | === Need a BAM Index File? ===
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− | Check your BAM files
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− | ls $SAMPLE/output/bams/*bam
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− | Check your BAI files
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− | ls $SAMPLE/output/bams/*bai
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− | Do you have the same number of BAM & BAI files?
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− | * If so, then you are good to go.
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− | * If you have more BAI's than BAM's - oops!!! (LET ME KNOW)
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− | * If you have more BAM's than BAI's, we need to generate the index:
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− | *: <pre>$GC/bin/samtools index $SAMPLE/output/bams/YOUR_BAM_WITH_MISSING_BAI.bam</pre>
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| === Detach From screen=== | | === Detach From screen=== |