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what's difference between a read marked by "sam FLAG 1024" and marked by " PG:markduplicates" ?


    1 . when I  run the following command :
         "samtools view -h -f 1024  bwa.raw.bam  " ,  then can not get any reads , so I think BWA do not markduplicates to use" FLAG 1024".  
    2   after I  deal with  bwa.raw.bam with using picard-markduplicates , 
          "samtools view -h -f 1024  baw.raw.markdup.bam  "   , I got some reads with the below marks : 
               FLAG : 1187    PG:Z:MarkDuplicates
     SO  i got a question : 
                I know  the option "-f  1024"  is just for optical or pcr dups , but  I do not know which software modify "FLAG"  to add "1024"  ??
               according to 1 , I think BWA do not do that becasue  no reads found . 
               however ,according to 2 , I got reads markd by "FLAG 1024", so I guess   when I do  the picard-markduplicates step , picard will modify sam flag  ?? ,not just add "PG:Z:MarkDuplicates" .

Best Answer

  • YingLiuYingLiu China
    Accepted Answer

    @YingLiu said:

    @YingLiu said:
    maybe the FLAG value "1024" is added by samtools ??

    I made some tests .
    I feel Picard-Markduplicates will correct sam FLAG value to plus 1024 if judge this read as duplicates read , and will insert a mark
    "PG:Z:Markduplicates" for every read .


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