Changes

SeqShop: Calling Your Own Genome, May 2015 (view source)

433 bytes removed , 22:12, 18 May 2015

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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===

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