Dear All,
I am facing some big problem with samtools rmdup command,
What I would like to do is to discard reads that fail to align as proper pairs and remove non-unique fragments (and not non-unique reads), in order to delete paired reads that have both F and R reads starting and ending exactly in the same place.
I tried to run:
to select only properly paired reads
to remove duplicates:
but it seems thta reads are not properly removed,
I tried also to run samtools fixmate before running rmdup but even strangest results.
So I Switched to Piacard tools Markduplicates command:
But even if my file is sorted the program fails reporting bam not sorted:
Any suggestion??
Thanks,
Paolo
I am facing some big problem with samtools rmdup command,
What I would like to do is to discard reads that fail to align as proper pairs and remove non-unique fragments (and not non-unique reads), in order to delete paired reads that have both F and R reads starting and ending exactly in the same place.
I tried to run:
to select only properly paired reads
Code:
samtools view -f 2 -b -h -o output.bam input.bam
Code:
samtools rmdup input.bam output.bam
I tried also to run samtools fixmate before running rmdup but even strangest results.
So I Switched to Piacard tools Markduplicates command:
Code:
java -jar MarkDuplicates.jar I=input.bam O=output.bam M=marked_rep ort.txt VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=true
Exception in thread "main" net.sf.picard.PicardException: Input file input.bam is not coordinate sorted.
Thanks,
Paolo
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