Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

why do BaseRecalibrator read counts differ?

biscuit13161biscuit13161 Posts: 11Member

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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