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21
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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 7 months ago by Charlotte.Herzeel • 140
0
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0
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289
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0
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picard markduplicate output smaller file
gatk picard markduplicates bioinformatics written 4 months ago by Peter Chung • 80
1
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1
answer
365
views
1
answer
Warning in GATK Picard MarkDuplicates
variant calling gatk picard markduplicates written 6 months ago by Mehulsharma.253 • 10 • updated 6 months ago by Pierre Lindenbaum ♦ 120k
7
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1
answer
1.3k
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1
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Is there an authoritative source for optional BAM tags?
duplicates picard markduplicates bam written 3.3 years ago by John ♦ 12k • updated 9 months ago by RamRS ♦ 21k
6
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1
answer
647
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1
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How to interpret the "Matrics" file of MarkDuplicates (Picard)
picard markduplicates written 9 months ago by ravipatel4 • 10
2
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1
answer
572
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1
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GATK MarkDuplicates output and bam
gatk markduplicates written 10 months ago by bioguy24 • 190 • updated 10 months ago by finswimmer ♦ 11k
3
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1
answer
845
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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 11 months ago by salamandra • 200
0
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2
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896
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2
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Picard MarkDuplicates flag vs remove issue
duplicates picard atac-seq markduplicates written 12 months ago by s1469060 • 10 • updated 12 months ago by Prakash • 1.2k
2
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1
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1.6k
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1
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Picard Mark Duplicates
picard markduplicates written 14 months ago by Varun Gupta • 1.1k • updated 12 months ago by marcela.uliano • 50
2
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1
answer
685
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1
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Picard MarkDuplicates fatal error
picard markduplicates written 15 months ago by fwuffy • 50 • updated 15 months ago by h.mon ♦ 25k
5
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1
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3.2k
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1
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Gatk Pipeline: Markduplicates At The End ?
workflow next-gen pipeline gatk markduplicates duplicates bam written 6.6 years ago by Pierre Lindenbaum ♦ 120k • updated 20 months ago by Biostar ♦♦ 20
1
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1
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2.3k
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1
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Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 6.7 years ago by ian.streeter • 10 • updated 2.0 years ago by Biostar ♦♦ 20
2
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1
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1.3k
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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 2.1 years ago by lghust2011 • 90 • updated 2.1 years ago by Pierre Lindenbaum ♦ 120k
3
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0
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0
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picard MarkDuplicates find EOF problem
eof markduplicates written 2.1 years ago by victoria_aleks • 30
0
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1
answer
765
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1
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Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 2.2 years ago by James Ashmore • 2.6k
1
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0
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1.1k
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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 2.3 years ago by pentiumy • 10 • updated 2.3 years ago by Pierre Lindenbaum ♦ 120k
1
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1
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1.6k
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1
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Error in picard tool: Mark Duplicates
software error sam-input picard markduplicates written 2.3 years ago by jcanitz • 0 • updated 2.3 years ago by dariober ♦ 10k
3
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0
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1.1k
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0
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Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
picard markduplicates bam written 2.4 years ago by 14134125465346445 • 3.4k
3
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1
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2.5k
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1
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Picard Markduplicates output
next-gen picard markduplicates written 3.1 years ago by VasGene • 20 • updated 3.1 years ago by Amitm • 1.6k
0
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2
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3.4k
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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 3.3 years ago by nbhardwaj • 130 • updated 3.2 years ago by Peter Georgeson • 0
4
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1
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2.2k
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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 3.2 years ago by anp375 • 160 • updated 3.2 years ago by Matt Shirley ♦ 9.0k
1
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0
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3.9k
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0
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MarkDuplicates memory issue
alignment picard markduplicates written 3.4 years ago by cacampbell • 40
2
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2
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3.1k
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2
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Mark duplicates for single end reads: Why only 5'end?
read duplicates 5' 3'end markduplicates written 4.1 years ago by dariober ♦ 10k
4
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0
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1.3k
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0
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Is there software that takes advantage of MarkedDuplicates for SNP calling?
gatk markduplicates snp consensus sequence written 4.2 years ago by shuelga • 20
16
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4
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2.8k
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14 follow
4
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sam/bam file handling -> new tools?
bam sort markduplicates sam written 4.2 years ago by Richard • 550 • updated 4.2 years ago by lh3 ♦ 31k
2
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1
answer
1.9k
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1
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How does samblaster use library tag information if at all?
markduplicates samblaster written 4.7 years ago by Carlos Borroto • 1.8k • updated 4.3 years ago by gf4ea • 30
9
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1
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4.9k
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5 follow
1
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Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
picard samtools markduplicates bam sort written 5.1 years ago by Jordan • 1.1k • updated 4.5 years ago by 1013002214 • 0
9
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2
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11k
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2
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Markduplicates: Value Was Put Into Pairinfomap More Than Once
picard markduplicates written 6.4 years ago by lifuqiang0611 • 20 • updated 4.6 years ago by karl.stamm ♦ 3.5k
5
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2
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2.5k
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2
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markDuplicates: Histogram not produced
picard markduplicates written 4.7 years ago by dariober ♦ 10k
5
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1
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3.6k
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1
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Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does not equal value computed..."
picard markduplicates sam validation error written 4.8 years ago by Mark Ebbert • 70 • updated 4.8 years ago by lomereiter • 430
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