Hi,

I have a BAM file which has chr id's as `NC_00000*.` I did sorting using samtools sort function.

I wanted to remove duplicates, so I'm using MarkDuplicates.jar from Picard tools to get the job done. But it gives me the following error:

    Exception in thread "main" net.sf.picard.PicardException: 13_0501.sorted.bam is not coordinate sorted.
       at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:273)
       at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:117)
       at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
       at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:101)

But I think my bam file is sorted. This is the header of my bam file.

    @HD     VN:1.0  SO:unsorted
    @SQ     SN:NC_000001    LN:249250621
    @SQ     SN:NC_000002    LN:243199373
    @SQ     SN:NC_000003    LN:198022430
    @SQ     SN:NC_000004    LN:191154276
    @SQ     SN:NC_000005    LN:180915260
    @SQ     SN:NC_000006    LN:171115067
    @SQ     SN:NC_000007    LN:159138663
    @SQ     SN:NC_000008    LN:146364022
    @SQ     SN:NC_000009    LN:141213431
    @SQ     SN:NC_000010    LN:135534747
    @SQ     SN:NC_000011    LN:135006516
    @SQ     SN:NC_000012    LN:133851895
    @SQ     SN:NC_000013    LN:115169878
    @SQ     SN:NC_000014    LN:107349540
    @SQ     SN:NC_000015    LN:102531392
    @SQ     SN:NC_000016    LN:90354753
    @SQ     SN:NC_000017    LN:81195210
    @SQ     SN:NC_000018    LN:78077248
    @SQ     SN:NC_000019    LN:59128983
    @SQ     SN:NC_000020    LN:63025520
    @SQ     SN:NC_000021    LN:48129895
    @SQ     SN:NC_000022    LN:51304566
    @SQ     SN:NC_000023    LN:155270560
    @SQ     SN:NC_000024    LN:59373566
    @PG     ID:0    PN:clcgenomicswb        VN:7.0

The header seems to suggest that it's unsorted. That's what is bothering me.
your SAM Header starts with:

    @HD     VN:1.0  SO:unsorted

And Picard check that this 'SO:' is set to 'coordinate'. See https://github.com/nh13/picard/blob/master/src/java/net/sf/picard/sam/MarkDuplicates.java

    (....)
     if (!ASSUME_SORTED && header.getSortOrder() != SortOrder.coordinate) {
                    throw new PicardException("Input file " + f.getAbsolutePath() + " is not coordinate sorted.");
                }

to fix this, use the option

    ASSUME_SORTED=true