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09-08-2015, 09:04 AM
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#1 |
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Registered Vendor
Location: Illinois, USA Join Date: Mar 2013
Posts: 18
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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? Thanks, Nik |
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09-08-2015, 09:41 AM
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#2 |
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Senior Member
Location: Bethesda MD Join Date: Oct 2009
Posts: 509
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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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| Tags |
| gatk indelrealigner, samtools, variant detection |
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