Picard

[bair]

Hello all,

I merged two ELAND export files by using samtools, but samtools flagstat shows that

191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)

Why it shows 0 properly paired?

Couldn't run picard MarkDuplicates, thread exception:

Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

Any help? Many thanks.

[nilshomer]

Hello all,

I merged two ELAND export files by using samtools, but samtools flagstat shows that

191134982 in total
0 QC failure
0 duplicates
139825529 mapped (73.16%)
191134982 paired in sequencing
95567491 read1
95567491 read2
0 properly paired (0.00%)
115989136 with itself and mate mapped
23836393 singletons (12.47%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)

Why it shows 0 properly paired?

It looks like the converter did not set the "properly paired" bit in the FLAG field.

Couldn't run picard MarkDuplicates, thread exception:

Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105)

Any help? Many thanks.

Looks like a bug to me.

Send both to [email protected]

[Lv Ray]

I got the same error. Have you solved your problem, bair or nilshomer?