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-   -   Using GATK's local realigner outside of GATK pipeline for variant calling (http://seqanswers.com/forums/showthread.php?t=62545)

NikTuzov 09-08-2015 09:04 AM

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

HESmith 09-08-2015 09:41 AM

No problem - in fact, the latest version of SAMtools variant-calling workflow uses GATK's realigner and base recalibrator.


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