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6 votes
Accepted

How many false positive duplicates are marked using just the position of first unclipped base?

There's a tool in Picard (full disclaimer: I wrote it...) called CollectIndependentReplicateMetrics which performs the test you are looking for, I think. It measures the percent of duplication that is ...
Yossi Farjoun's user avatar
6 votes

Does picard markduplicate toggle PCR duplicate samflag

Yes, if MarkDuplicates encounters a pair that's marked as a duplicate that it considers (for whatever reason) to not be a duplicate then it will unset the duplicate mark. You can test this yourself by ...
Devon Ryan's user avatar
  • 19.6k
3 votes

Targeted NGS, up to 99% of reads have been marked as duplicates

If you're doing target capture, especially of a small region, it is entirely possible that there are only five unique reads. Target capture is molecularly finicky and sometimes the entire region is ...
conchoecia's user avatar
  • 3,181
2 votes

How does picard's MarkDuplicate handle unmapped reads?

From the Picard documentation: DUPLICATION METRICS: Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords. UNMAPPED_READS The total number of unmapped ...
James Hawley's user avatar
  • 1,384
1 vote

MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

You need to set your Java version to Java 8. If you are using conda, run this in your conda environment: conda install openjdk=8
Anton Esibov's user avatar
1 vote

Impact of merging ChIP-seq runs of the same sample on PCR duplicates identification?

If you are sequencing same library multiple times (as you state in the question), any read that appears in multiple sequencing runs is likely to have been generated via PCR duplication from the same ...
Ian Sudbery's user avatar
  • 3,321
1 vote

Diploid Consensus Sequences

How to separate reads, one for each reference haplotype. Map all the reads against the reference genome Use GATK to call SNPs Use GATK tool [FastaAlternateReferenceMaker][1] to build the alternative ...
Fabio Marroni's user avatar
1 vote
Accepted

Targeted NGS, up to 99% of reads have been marked as duplicates

Most duplicate marking programs do it by looking at the start and end location of hits. In this case, if two reads have identical start and end locations for both reads, then they will be considered [...
gringer's user avatar
  • 14.3k

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