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why do BaseRecalibrator read counts differ?

biscuit13161biscuit13161 QatarPosts: 13Member

following on from Pallavi's question "I Don't understand what is filtering out during traversal ", can you explain why the number of processed reads ("INFO 02:09:56,512 BaseRecalibrator - Processed: 1059663038 reads" from Pallavi's example) differs so much from the total number of reads ("INFO 02:09:56,514 MicroScheduler - 25351 reads were filtered out during traversal out of 45356 total"). Do these numbers relate to different sets of reads?

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