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Picard MarkDuplicates flag vs remove issue
duplicates picard atac-seq markduplicates written 5 days ago by s1469060 • 10 • updated 5 days ago by prakash • 120
2
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1
answer
240
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1
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Picard Mark Duplicates
picard markduplicates written 8 weeks ago by Varun Gupta • 1000 • updated 20 days ago by marcela.uliano • 30
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1
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224
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1
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Picard MarkDuplicates fatal error
picard markduplicates written 3 months ago by fwuffy • 50 • updated 3 months ago by h.mon ♦ 15k
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1
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2.8k
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1
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Gatk Pipeline: Markduplicates At The End ?
workflow next-gen pipeline gatk markduplicates duplicates bam written 5.6 years ago by Pierre Lindenbaum ♦ 108k • updated 7 months ago by Biostar ♦♦ 20
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1
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Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 5.7 years ago by ian.streeter • 10 • updated 12 months ago by Biostar ♦♦ 20
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1
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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 13 months ago by lghust2011 • 70 • updated 13 months ago by Pierre Lindenbaum ♦ 108k
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560
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picard MarkDuplicates find EOF problem
eof markduplicates written 13 months ago by victoria_aleks • 30
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1
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475
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1
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Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 14 months ago by James Ashmore • 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 15 months ago by pentiumy • 10 • updated 15 months ago by Pierre Lindenbaum ♦ 108k
1
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Error in picard tool: Mark Duplicates
software error sam-input picard markduplicates written 16 months ago by jcanitz • 0 • updated 16 months ago by dariober ♦ 9.1k
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Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
picard markduplicates bam written 16 months ago by 14134125465346445 • 3.4k
3
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1
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1.5k
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1
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Picard Markduplicates output
next-gen picard markduplicates written 2.1 years ago by VasGene • 10 • updated 2.1 years ago by Amitm • 1.5k
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Picard MarkDuplicates error: Value was put into PairInfoMap more than once
bedtools picard samtools markduplicates written 2.4 years ago by nbhardwaj • 100 • updated 2.2 years ago by Peter Georgeson • 0
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1.5k
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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 2.2 years ago by anp375 • 140 • updated 2.2 years ago by Matt Shirley ♦ 8.4k
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1
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996
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1
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Is there an authoritative source for optional BAM tags?
duplicates picard markduplicates bam written 2.3 years ago by John ♦ 12k
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0
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MarkDuplicates memory issue
alignment picard markduplicates written 2.4 years ago by cacampbell • 40
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2
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2.4k
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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 3.2 years ago by dariober ♦ 9.1k
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Is there software that takes advantage of MarkedDuplicates for SNP calling?
gatk markduplicates snp consensus sequence written 3.2 years ago by shuelga • 20
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4
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14 follow
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sam/bam file handling -> new tools?
bam sort markduplicates sam written 3.3 years ago by Richard • 530 • updated 3.3 years ago by lh3 ♦ 30k
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1
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1.6k
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1
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How does samblaster use library tag information if at all?
markduplicates samblaster written 3.7 years ago by Carlos Borroto • 1.7k • updated 3.3 years ago by gf4ea • 30
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1
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4.1k
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5 follow
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Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
picard samtools markduplicates bam sort written 4.2 years ago by Jordan • 1.0k • updated 3.6 years ago by 1013002214 • 0
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2
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9.8k
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2
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Markduplicates: Value Was Put Into Pairinfomap More Than Once
picard markduplicates written 5.5 years ago by lifuqiang0611 • 20 • updated 3.6 years ago by karl.stamm ♦ 3.2k
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markDuplicates: Histogram not produced
picard markduplicates written 3.7 years ago by dariober ♦ 9.1k
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1
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3.1k
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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 3.8 years ago by Mark Ebbert • 70 • updated 3.8 years ago by lomereiter • 410
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3
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2.7k
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7 follow
3
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Tool to unmark duplicates
picardtools samtools markduplicates pcr duplicates written 3.9 years ago by Mark Ebbert • 70 • updated 3.9 years ago by Pierre Lindenbaum ♦ 108k
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Picard MarkDuplicates and SamTools rmdup algorithm documentation
picard samtools markduplicates rmdup written 4.0 years ago by Mark Ebbert • 70 • updated 4.0 years ago by Pierre Lindenbaum ♦ 108k
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2.1k
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Will Picard MarkDuplicates also un-mark duplicates?
duplicates ngs picard markduplicates bam written 4.0 years ago by Chris Miller ♦ 19k • updated 4.0 years ago by Pierre Lindenbaum ♦ 108k
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1.1k
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Adding Unpaired_Reads_Examined And Read_Pairs_Examined In Metrics Of Picard Markduplicates
picard markduplicates written 4.3 years ago by chunxuan • 10
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1
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8.8k
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1
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Library Duplicates Vs. Optical Duplicates (Picard Markduplicates)
picard markduplicates bam written 6.7 years ago by toni • 2.1k • updated 4.5 years ago by Biostar ♦♦ 20
8
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3.7k
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7 follow
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Duplication Removing Using Filtering Xt:A:U, Samtools -Rmdup And Picard Markduplicates
picard samtools markduplicates written 4.7 years ago by Tonyzeng • 280 • updated 4.6 years ago by geek_y ♦ 8.6k
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