Could you please provide a place where I can copy them to? Thanks!
From: Nils Homer [mailto:nho...@broadinstitute.org]
Sent: Thursday, October 16, 2014 1:20 PM
To: Salzberg, Anna
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard
MarkDuplicates
Hey Anna,
could you provide me with the inputs (i.e BAM and FASTA) to the MarkDuplicates
tool so we can reproduce and debug? Having a reduced test case would be ideal
as I cannot debug easily from the information you provided. Thanks!
Nils
On Thu, Oct 16, 2014 at 1:10 PM, Salzberg, Anna
<asalzb...@hmc.psu.edu<mailto:asalzb...@hmc.psu.edu>> wrote:
Nils,
I have identified a bug with optical duplicates that is not fixed in picard v
1.122.
In particular, I ran bwa and then picard MarkDuplicates on lane 1 and lane 2
files separately, and I then did the same for the merged fastq files. I got
the picard MarkDuplicates results below. Note that the overall % duplication
is higher in the merged file than in the individual lane ones (to be expected),
but that the OPTICAL duplicates is also higher, that is, it is more than the
sum of the OPTICAL duplicates of lanes 1 and 2 (NOT to be expected).
In other words, it is expected that the overall duplication is higher than the
sum of the ones in lanes 1 and 2 due to interaction between the reads of lanes
1 and 2 (for ex., read1 from lane1 could have no duplicates in lane1, and read2
from lane2 could have no duplicate in lane2 but in the merged file they could
be duplicates of each other). However, by definition, there should be no
interaction in the OPTICAL duplicates between lanes 1 and 2, and therefore the
results below seem wrong. My suspicion is that the MarkDuplicates optical
duplication algorithm is not checking for the lane.
Sample LIBRARY UNPAIRED_READS_EXAMINED
READ_PAIRS_EXAMINED UNMAPPED_READS
UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES
READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION
ESTIMATED_LIBRARY_SIZE
A_merged Unknown Library 497938 21072701
939669 326848 9821728 3875890 0.46831
18726206
A_L1 Unknown Library 247592 10518632
458565 141958 3109570<tel:3109570> 1074927
0.298856 18640119
A_L2 Unknown Library 250347 10554068
481105 147968 3130326 1080576 0.30005
18605087
Thank you for looking into this!
Anna
From: Salzberg, Anna
Sent: Friday, October 10, 2014 11:33 AM
To: 'Nils Homer'
Cc:
'samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>'
Subject: RE: [Samtools-help] Reporting Bug - Optical Duplicates of Picard
MarkDuplicates
Nils,
I see I made a mistake in my countTileDups script, in that I report the wrong
variable in the end!! The number of dups in the same tile is in fact > than
you reported optical duplicates.
So please ignore my request for now.
Thank you,
Anna
From: Salzberg, Anna
Sent: Friday, October 10, 2014 10:26 AM
To: 'Nils Homer'
Cc:
samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>
Subject: RE: [Samtools-help] Reporting Bug - Optical Duplicates of Picard
MarkDuplicates
Dear Nils,
I installed Picard 1.122, and the number of optical duplicates was reduced by
over 25% (the estimated library size was also different in the new version).
Unfortunately, I still think that there is a bug with the number of optical
duplicates, as simply counting the number of duplicates that have the same tile
results in 3 orders of magnitude less than the MarkDuplicates optical
duplicates count.
I would *greatly* appreciate if you could look into this as this is super
important to my lab. I have provided in my previous email 2 scripts; one of
them is a very simple script (only a few lines) that simply counts duplicates
with the same tile.
Thank you very much for your help with this issue.
Anna
From: Nils Homer [mailto:nho...@broadinstitute.org]
Sent: Thursday, October 09, 2014 4:34 PM
To: Salzberg, Anna
Cc:
samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>
Subject: Re: [Samtools-help] Reporting Bug - Optical Duplicates of Picard
MarkDuplicates
I am replying to the list so others can benefit from our discussion.
The latest Picard release to support updated Illumina read names is 1.120 while
your install is 1.99. You will need to update to this version or the latest
version to get the benefit of this update.
Nils
On Thu, Oct 9, 2014 at 4:08 PM, Nils Homer
<nho...@broadinstitute.org<mailto:nho...@broadinstitute.org>> wrote:
Could you tell us what version of Picard you are using? There was an issue
earlier with parsing read names from newer Illumina analysis software.
Nils
On Thu, Oct 9, 2014 at 3:00 PM, Salzberg, Anna
<asalzb...@hmc.psu.edu<mailto:asalzb...@hmc.psu.edu>> wrote:
Hello,
I am convinced that the optical duplicates count of the Picard MarkDuplicates
command is incorrect. When I wrote a script to detect optical duplicates in
my dataset, I got only ~1k optical duplicates as opposed to MarkDuplicates ~3
million. I think the problem with MarkDuplicates is tile related because I
then wrote a super simple script that simply counts how many duplicates share
the same tile, and that was < 4k, that is, 3 orders of magnitudes less than
MarkDuplicates! The overall number of duplicates (opticals or otherwise)
matched (~7 million). I'm convinced my script is right, as it's so simple.
Remove optical duplicates script:
https://gist.github.com/annasa/eef7c30152ac296bb49b
Count duplicates in same tile:
https://gist.github.com/annasa/f5633eecf012153a3ff2
Both scripts take as input a sam file sorted on chr and startPos. They also
assume that when the sequence name is parsed by ":" then the tile is the 5th
field, x the 6th and y the 7th (e.g. HWI-ST1318:119:H89A3ADXX:1:2209:1705:6933,
where tile is '2209', x is '1705' and y is'6933'). Finally, they assume that
the file is for a single lane, as I was working with such files.
This is VERY important for my lab. Please advise as soon as you can.
Thank you,
Anna
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