Hi all,
I have a set of amplicon target sequencing libraries and I am trying to generate some basic metrics (e.g. number of reads, coverage of amplicons, etc) using the Picard Tools CollectTargetedPcrMetrics.jar. What I've noticed is that the tool ignores reads which have been marked as duplicates in its calculation of the statistics such as coverage of an amplicon. I was wondering if there was a way to get CollectTargetedPcrMetrics to ignore PCR duplicates. I wasn't able to find any parameters about this ...
The libraries have been aligned with bwa and then mark duplicate. I suppose one option could be to not mark duplicates, but that seems like a roundabout way of solving this.
Anyone else encountered this question before? Also, while we are on the topic what is the difference in the amplicon interval list and the target interval list? The reason I ask is that I passed in my intervals list file to the PER_TARGET_COVERAGE parameter and I ended up getting negative mean coverage which doesn't make sense to me (I didn't mark duplicates for this one). Anyone encountered this?
Thanks,
I have a set of amplicon target sequencing libraries and I am trying to generate some basic metrics (e.g. number of reads, coverage of amplicons, etc) using the Picard Tools CollectTargetedPcrMetrics.jar. What I've noticed is that the tool ignores reads which have been marked as duplicates in its calculation of the statistics such as coverage of an amplicon. I was wondering if there was a way to get CollectTargetedPcrMetrics to ignore PCR duplicates. I wasn't able to find any parameters about this ...
The libraries have been aligned with bwa and then mark duplicate. I suppose one option could be to not mark duplicates, but that seems like a roundabout way of solving this.
Anyone else encountered this question before? Also, while we are on the topic what is the difference in the amplicon interval list and the target interval list? The reason I ask is that I passed in my intervals list file to the PER_TARGET_COVERAGE parameter and I ended up getting negative mean coverage which doesn't make sense to me (I didn't mark duplicates for this one). Anyone encountered this?
Thanks,
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