Re: [Samtools-help] MarkDuplicates minor bug

[Alec W. <al...@br...>]

Hi Jessica,

Can you clarify a couple of things?  When you say "the two files seem to 
match," what two files are you referring to?  When the two files are 
slightly off, what does that mean?

Thanks, Alec

On 8/24/10 9:45 AM, Jessica Maia wrote:
> Hi there,
>
> I think there's a minor bug in Picard's MarkDuplicates function. Reads were aligned with BWA and variants identified with Samtools. I ran the following steps 4 times in this order with only the merge step being different among runs:
>
> aln
> sampe/samse
> import
> sort
> merge
> -Samtools merge version1 - merged all the individual bam files for each lane all at once
> -Samtools merge version2 - merge the files for each Illumina run first, then then merged bam files for all the runs into 1 file.
> Picard's MarkDuplicates with REMOVE_DUPLICATES=true
> pileup -c
> varFilter.
>
> After the merge step and before the PCR duplicate removal, I ran Picard's AlignmentSummaryMetrics and the two files seem to match. After the PCR duplicate removal step, I ran AlignmentSummaryMetrics and the two files are slightly off. In addition, the snp/indels obtained at the end are slightly off.
>
> The second time I ran these steps, I sorted the bam files after the merge step and before PCR duplicate removal. This produced the same outcome had I not sorted before removing duplicates.
>
> I'm happy to provide more details. The bam files are quite large, about 140G, corresponding to about 1.5  billion reads.
>
>
> Jessica
>
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