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Old 09-08-2015, 09:04 AM   #1
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Default Using GATK's local realigner outside of GATK pipeline for variant calling

Hello all:

If I were to use GATK's local realigner outside of GATK pipeline, eg:

BWA -> GATK's Local Realigner -> SAMTools

then will I have any extra problems because I use non-GATK modules upstream or downstream of realignment?

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Old 09-08-2015, 09:41 AM   #2
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No problem - in fact, the latest version of SAMtools variant-calling workflow uses GATK's realigner and base recalibrator.

Last edited by HESmith; 09-08-2015 at 12:22 PM. Reason: typo
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gatk indelrealigner, samtools, variant detection

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