Hello,
here is my problem ! I run picard MarkDuplicates with REMOVE_DUPLICATES=true. And I thought that remove pcr and optical duplicates. But it doesn't work. I dont know what the problem is. But this are duplicates or ? samtools rmdup remove these duplicates.. It seems that picard cluster the duplicates but don't remove these duplicates..
Is this a bug or what is wrong ?
FCC0WRYACXX:1:1212:8677:81169 99 1 14405 1 100M = 14489 183 TTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACA @CCFFFFFHHHHDGIIJJJGCDJGDEEHIDGHCAGGIIEFHHCFHHCFHIGHIIJGGEHEHGHJIIGEAB6BCCDCB;<BCBB?BDBDDDDDCC>ACBBD PG:Z:MarkDuplicates NH:i:4 HI:i:1 nM:i:0 AS:i:197
FCC0WRYACXX:1:1213:5301:23125 419 1 14405 1 100M = 14492 187 TTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACA @BCFDEFFHHFHFIIJIIJJIIIGGFHHHGIEFHGJJIJGGGGIGHHGJJEFFHEGIGHHIFCFGGIHHFFFEDC5;?BDD@DBDDDDDBB?9>CB?BBC PG:Z:MarkDuplicates NH:i:4 HI:i:3 nM:i:0 AS:i:198
FCC0WRYACXX:1:1308:4376:65126 99 1 14405 1 100M = 14491 186 TTCTGCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCCCA @@@FFFFFHHHHDIHIEFGFHIIIIAHFDHHHHIIJGIIIJIGIGIJJJJJJGIJJJIIIJ@CHGGAEAB<>ABD??B5?CDBB5<>ABD9CCD:<C(<A PG:Z:MarkDuplicates NH:i:4 HI:i:1 nM:i:1 AS:i:196
1 answer
First: It is better to read the documentation before posting a question
Second: Stick to picard markduplicates for this, not sam remdup
Third: This is what you are looking for...
https://broadinstitute.github.io/picard/command-line-overview.html
"The program can take either coordinate-sorted or query-sorted inputs, however the behavior is slightly different. When the input is coordinate-sorted, unmapped mates of mapped records and supplementary/secondary alignments are not marked as duplicates. However, when the input is query-sorted (actually query-grouped), then unmapped mates and secondary/supplementary reads are not excluded from the duplication test and can be marked as duplicate reads."
Your result is dependent on: 1) how you sort 2) whether you want to keep or remove unmapped mates
I would suggest sorting by coordinate and removing unmapped mates before running picard mark duplicates.
How to do this?..... read about SAM flags and use the command line.
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maybe picard flag unmapped duplicates but dont remove them ?
If the mate is mapped at a different location, a pair is not a duplicate...
I had reading that a mate paire is a duplicate if they have the same start position and they have all the same start position
The mate position is different, though. So they are not duplicates and you would not want to remove them.