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Sorting by reference index seems doesn't work or sorted by DESC order ? #1204

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liamlee opened this Issue Oct 11, 2016 · 2 comments

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liamlee commented Oct 11, 2016

I use method sortReadsByReferencePositionAndIndex() to sort my record and then save to sam/bam file, the results show like the pitch blow ,the order seems to be DESC ?

val sortedRDD = alignmentRecordRDD.sortReadsByReferencePositionAndIndex()
val markRDD = sortedRDD.markDuplicates()
markRDD.saveAsSam(...)

qq20161011-0 2x

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liamlee Oct 11, 2016

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Maybe I should do sort after markDuplicates()

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liamlee commented Oct 11, 2016

Maybe I should do sort after markDuplicates()

@liamlee liamlee closed this Oct 11, 2016

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fnothaft Oct 11, 2016

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Thanks for pinging this @liamlee! Duplicate marking will group reads by fragment, so you do need to run sort after duplicate marking.

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fnothaft commented Oct 11, 2016

Thanks for pinging this @liamlee! Duplicate marking will group reads by fragment, so you do need to run sort after duplicate marking.

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