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== Alignment Pipeline FAQs ==
== Alignment Pipeline FAQs ==
; Error "read <> mapped to 'chr1' at POS 0 to -1, flag 69,0 has BIN 4680 but should be 266824".<br /> "Fix it by using BAM->SAM->BAM to force a recalculation of the BIN field."<br /> "Fail to index the BAM file"
:This error appears to be due to BWA reference files that do not match the version of BWA used to run GotCloud align. Run the following to regenerate the BWA reference files with the GotCloud version of BWA.
::<pre>gotcloud/bin/bwa index path/to/your/ref.fa</pre>
== Variant Calling Pipeline FAQs ==
== Variant Calling Pipeline FAQs ==
