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20
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2
answers
15k
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10 follow
2
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Understanding Samtools Flagstat Output
illumina paired-end picard samtools markduplicates written 6.1 years ago by geek_y ♦ 10.0k • updated 4 days ago by Nitha • 10
0
votes
0
answers
130
views
0
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GATK MarkDuplicatesSpark Space Issues
gatk markduplicates written 10 weeks ago by aalith • 10
6
votes
2
answers
296
views
2
answers
samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
samtools atac-seq markduplicates written 3 months ago by nanoide • 30 • updated 3 months ago by predeus • 1.2k
21
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2
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1.4k
views
5 follow
2
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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 12 months ago by Charlotte.Herzeel • 140
0
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0
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465
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0
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picard markduplicate output smaller file
gatk picard markduplicates bioinformatics written 9 months ago by Peter Chung • 80
1
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1
answer
606
views
1
answer
Warning in GATK Picard MarkDuplicates
variant calling gatk picard markduplicates written 11 months ago by Mehulsharma.253 • 10 • updated 11 months ago by Pierre Lindenbaum ♦ 124k
7
votes
1
answer
1.5k
views
1
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Is there an authoritative source for optional BAM tags?
duplicates picard markduplicates bam written 3.7 years ago by John ♦ 12k • updated 14 months ago by RamRS ♦ 24k
7
votes
1
answer
898
views
1
answer
How to interpret the "Matrics" file of MarkDuplicates (Picard)
picard markduplicates written 14 months ago by ravipatel4 • 50
2
votes
1
answer
785
views
1
answer
GATK MarkDuplicates output and bam
gatk markduplicates written 15 months ago by bioguy24 • 190 • updated 15 months ago by finswimmer ♦ 12k
3
votes
1
answer
1.3k
views
1
answer
Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with commandline/with R dupRadar package
picard markduplicates rna-seq written 16 months ago by salamandra • 240
0
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2
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1.2k
views
2
answers
Picard MarkDuplicates flag vs remove issue
duplicates picard atac-seq markduplicates written 17 months ago by s1469060 • 10 • updated 17 months ago by Prakash • 1.7k
2
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1
answer
2.1k
views
1
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Picard Mark Duplicates
picard markduplicates written 19 months ago by Varun Gupta • 1.1k • updated 17 months ago by marcela.uliano • 60
4
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1
answer
958
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1
answer
Picard MarkDuplicates fatal error
picard markduplicates written 20 months ago by fwuffy • 90 • updated 20 months ago by h.mon ♦ 28k
5
votes
1
answer
3.3k
views
1
answer
Gatk Pipeline: Markduplicates At The End ?
workflow next-gen pipeline gatk markduplicates duplicates bam written 7.0 years ago by Pierre Lindenbaum ♦ 124k • updated 2.1 years ago by Biostar ♦♦ 20
1
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1
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2.4k
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1
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Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 7.1 years ago by ian.streeter • 10 • updated 2.4 years ago by Biostar ♦♦ 20
2
votes
1
answer
1.5k
views
1
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Split the bam file by chromosome and speed up picard Markduplicates
next-gen alignment markduplicates sequencing written 2.5 years ago by lghust2011 • 90 • updated 2.5 years ago by Pierre Lindenbaum ♦ 124k
3
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0
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1.2k
views
0
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picard MarkDuplicates find EOF problem
eof markduplicates written 2.5 years ago by victoria_aleks • 30
0
votes
1
answer
873
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1
answer
Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 2.6 years ago by James Ashmore • 2.7k
1
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0
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1.4k
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0
answers
Picard: Value was put into PairInfoMap more than once. Even bwa enabled -M
next-gen picard markduplicates bwa written 2.7 years ago by pentiumy • 10 • updated 2.7 years ago by Pierre Lindenbaum ♦ 124k
1
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1
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1.8k
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1
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Error in picard tool: Mark Duplicates
software error sam-input picard markduplicates written 2.7 years ago by jcanitz • 0 • updated 2.7 years ago by dariober ♦ 10k
3
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0
answers
1.2k
views
0
answers
Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
picard markduplicates bam written 2.8 years ago by 14134125465346445 • 3.5k
3
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1
answer
3.0k
views
1
answer
Picard Markduplicates output
next-gen picard markduplicates written 3.5 years ago by VasGene • 20 • updated 3.5 years ago by Amitm • 1.6k
0
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2
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3.6k
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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 3.8 years ago by Floydian_slip • 130 • updated 3.6 years ago by Peter Georgeson • 0
4
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1
answer
2.4k
views
1
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Problem using PicardTools MarkDuplicates: Value Was Put Into Pairinfomap More Than Once
pairinfomap picard picardtools markduplicates written 3.6 years ago by anp375 • 170 • updated 3.6 years ago by Matt Shirley ♦ 9.2k
1
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0
answers
4.5k
views
0
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MarkDuplicates memory issue
alignment picard markduplicates written 3.8 years ago by cacampbell • 40
2
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2
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3.4k
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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 4.6 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 4.6 years ago by shuelga • 20
16
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4
answers
3.0k
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14 follow
4
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sam/bam file handling -> new tools?
bam sort markduplicates sam written 4.7 years ago by Richard • 570 • updated 4.7 years ago by lh3 ♦ 31k
2
votes
1
answer
2.0k
views
1
answer
How does samblaster use library tag information if at all?
markduplicates samblaster written 5.1 years ago by Carlos Borroto • 1.8k • updated 4.7 years ago by gf4ea • 30
9
votes
1
answer
5.2k
views
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 5.6 years ago by Jordan • 1.1k • updated 5.0 years ago by 1013002214 • 0
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