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markduplicates  (SourceForge net)

 
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    SourceForge net markduplicates
    Markduplicates, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/command+line+tool+markduplicates/markduplicates/pm38287052-63-2-9
    Average 90 stars, based on 1 article reviews
    markduplicates - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome
    Article Snippet: Before calling SNPs and small InDels, we used Picard ( http://sourceforge.net/projects/picard/ ) to filter the MarkDuplicates reads, then used GATK (v v3.2-2-gec30cee) ( ) to detect SNPs and small InDels.

    Polymerase Chain Reaction:

    Article Title: Disentangling the origins of viticulture in the western Mediterranean
    Article Snippet: .. PCR duplicates were removed with MarkDuplicates (http://picard.sourceforge.net) and reads with mapping qualities below 30 were removed. ..

    Article Title: Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits
    Article Snippet: The mapped reads were subsequently processed for format conversion (view), position sorting (sort), merging (merge), and statistics (stats) using Samtools ( http://samtools.sourceforge.net/ ). .. Then, the MarkDuplicates method from the Picard package ( https://sourceforge.net/projects/picard/ ) was used to remove the PCR duplicates that were introduced during library construction. ..

    Article Title: Stuttering associated with a pathogenic variant in the chaperone protein cyclophilin 40.
    Article Snippet: .. PCR duplicates were removed using MarkDuplicates from Picard (http://picard. sourceforge.net). .. Variant calling was performed with GATK (v.3.5) HaplotypeCaller and variant annotation run with ANNOVAR.10 Exome variants were filtered and selected according to the following criteria: location within a linkage region, genotype fitting the heterozygous dominant disease model, a minor allele frequency ≤ 0.01 according to the gnomAD (http://gnomad.broadinstitute.org) database, and variant type (missense, nonsense, coding indel or splice site variant).

    Article Title: Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.
    Article Snippet: .. Then, the MarkDuplicates method from the Picard package (https://sourceforge.net/ projects/picard/) was used to remove the PCR duplicates that were introduced during library construction. ..

    Software:

    Article Title:
    Article Snippet: .. The tool MarkDuplicates of the software package Picard (v.1.119 available at http://picard.sourceforge.net) was applied to mark and remove the optical duplicates from the alignments. ..



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