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22
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5 follow
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Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 2.4 years ago by Charlotte.Herzeel • 150
1
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0
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164
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GATK markduplicates / applyBQSR / haplotypecaller tools support unix pipe?
gatk unix pipe markduplicates applybqsr written 3 months ago by roccostorace • 30 • updated 10 weeks ago by Biostar ♦♦ 20
9
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1
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14k
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1
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What Is Pcr Duplicates Of Ngs?
duplicates markduplicates written 9.2 years ago by Bioscientist • 1.7k • updated 9 months ago by Biostar ♦♦ 20
1
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1
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511
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1
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Average depth/coverage before and after PCR duplicates cleanup
meandepth bam samtools markduplicates written 11 months ago by Begonia_pavonina • 20 • updated 9 months ago by Biostar ♦♦ 20
4
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0
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231
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5 follow
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Picard MarkDuplicates tool on a pooled sample BAM
illumina picard markduplicates written 12 months ago by joneill4x • 110
0
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0
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833
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0
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Problems with picard markduplicates
picard samtools markduplicates written 15 months ago by Cecelia • 20 • updated 15 months ago by Biostar ♦♦ 20
22
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2
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19k
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13 follow
2
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Understanding Samtools Flagstat Output
illumina paired-end picard samtools markduplicates written 7.4 years ago by geek_y ♦ 11k • updated 15 months ago by Nitha • 10
0
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956
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0
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GATK MarkDuplicatesSpark Space Issues
gatk markduplicates written 18 months ago by aalith • 10
8
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2
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1.9k
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2
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samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
samtools atac-seq markduplicates written 19 months ago by nanoide • 60 • updated 19 months ago by predeus • 1.5k
0
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1.0k
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picard markduplicate output smaller file
gatk picard markduplicates bioinformatics written 2.1 years ago by Peter Chung • 120
1
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1
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1.6k
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1
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Warning in GATK Picard MarkDuplicates
variant calling gatk picard markduplicates written 2.2 years ago by Mehulsharma.253 • 10 • updated 2.2 years ago by Pierre Lindenbaum ♦ 134k
7
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1
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1.7k
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1
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Is there an authoritative source for optional BAM tags?
duplicates picard markduplicates bam written 5.0 years ago by John ♦ 12k • updated 2.5 years ago by Ram ♦ 32k
8
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1
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How to interpret the "Matrics" file of MarkDuplicates (Picard)
picard markduplicates written 2.5 years ago by ravipatel4 • 50
2
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1
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1.8k
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1
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GATK MarkDuplicates output and bam
gatk markduplicates written 2.6 years ago by bioguy24 • 200 • updated 2.6 years ago by finswimmer ♦ 14k
3
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1
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3.2k
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1
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Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with commandline/with R dupRadar package
picard markduplicates rna-seq written 2.7 years ago by salamandra • 360
0
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2
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2.5k
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2
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Picard MarkDuplicates flag vs remove issue
duplicates picard atac-seq markduplicates written 2.7 years ago by s1469060 • 10 • updated 2.7 years ago by Prakash • 2.1k
2
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1
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3.8k
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1
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Picard Mark Duplicates
picard markduplicates written 2.9 years ago by Varun Gupta • 1.2k • updated 2.8 years ago by marcela.uliano • 70
5
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1
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1.6k
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1
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Picard MarkDuplicates fatal error
picard markduplicates written 3.0 years ago by fwuffy • 100 • updated 3.0 years ago by h.mon ♦ 32k
5
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1
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3.8k
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1
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Gatk Pipeline: Markduplicates At The End ?
workflow next-gen pipeline gatk markduplicates duplicates bam written 8.3 years ago by Pierre Lindenbaum ♦ 134k • updated 3.4 years ago by Biostar ♦♦ 20
1
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Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 8.4 years ago by ian.streeter • 10 • updated 3.7 years ago by Biostar ♦♦ 20
2
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1
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1.9k
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1
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Split the bam file by chromosome and speed up picard Markduplicates
next-gen alignment markduplicates sequencing written 3.8 years ago by lghust2011 • 90 • updated 3.8 years ago by Pierre Lindenbaum ♦ 134k
3
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0
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1.7k
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0
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picard MarkDuplicates find EOF problem
eof markduplicates written 3.8 years ago by victoria_aleks • 30
0
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1
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1.2k
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1
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Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 3.9 years ago by James Ashmore • 3.1k
1
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0
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2.4k
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0
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Picard: Value was put into PairInfoMap more than once. Even bwa enabled -M
next-gen picard markduplicates bwa written 4.0 years ago by pentiumy • 10 • updated 4.0 years ago by Pierre Lindenbaum ♦ 134k
1
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1
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2.4k
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1
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Error in picard tool: Mark Duplicates
software error sam-input picard markduplicates written 4.0 years ago by jcanitz • 0 • updated 4.0 years ago by dariober ♦ 11k
3
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0
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Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
picard markduplicates bam written 4.1 years ago by 14134125465346445 • 3.5k
3
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1
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4.2k
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1
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Picard Markduplicates output
next-gen picard markduplicates written 4.8 years ago by VasGene • 20 • updated 4.8 years ago by Amitm • 2.1k
0
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2
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4.4k
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2
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Picard MarkDuplicates error: Value was put into PairInfoMap more than once
bedtools picard samtools markduplicates written 5.1 years ago by Floydian_slip • 140 • updated 4.9 years ago by Peter Georgeson • 0
4
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1
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2.9k
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1
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Problem using PicardTools MarkDuplicates: Value Was Put Into Pairinfomap More Than Once
pairinfomap picard picardtools markduplicates written 4.9 years ago by anp375 • 180 • updated 4.9 years ago by Matt Shirley ♦ 9.5k
1
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0
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6.9k
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0
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MarkDuplicates memory issue
alignment picard markduplicates written 5.1 years ago by cacampbell • 50
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