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Questions tagged [markduplicate]

A tool from the Picard toolkit to mark or remove optical or PCR duplicates in sequencing data.

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6 votes
1 answer

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

In the popular picard MarkDuplicates tool, a read is marked as a duplicate if it has the same position as another read starting from their first unclipped base in ...
Ricky's user avatar
  • 63
2 votes
1 answer

MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

I have been trying to follow the GATK Best Practice Workflow for 'Data pre-processing for variant discovery' ( This has all been run on ...
ABG's user avatar
  • 21
0 votes
1 answer

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

I'd like to a follow up question to this question related to merging fastq files for ChIP-seq. Let's assume we have one sample library that is re-sequenced two or three times in order to achieve a ...
Ni-Ar's user avatar
  • 1
0 votes
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Diploid Consensus Sequences

My goal is to generate a diploid consensus genome. By "diploid consensus", I mean that I want to merge all supporting reads for a genomic region into a single haplome such that the resulting ...
annabelperry's user avatar
4 votes
1 answer

How does picard's MarkDuplicate handle unmapped reads?

Our BAM files are created according to a "lossless" alignment procedure [1] from the Broad Institute GATK documenation and involves re-adding the ...
init_js's user avatar
  • 319
4 votes
2 answers

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

Currently I'm performing whole analysis (pipeline from *.fastq to *.vcf) of 41 samples (targeted NGS). I rely on GATK best practices, however with some modifications. I decided to use the following ...
Adamm's user avatar
  • 206
5 votes
1 answer

Does picard markduplicate toggle PCR duplicate samflag

I have a RNA-seq bam file and there are few reads that are puzzling me. According to the bam header, this bam file is sorted by coordinate, created using tophat and markduplicate step is not done. ...
svural's user avatar
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