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<prev • 48 results • page 1 of 2 • next >
7
votes
1
answer
1.1k
views
1
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Is there an authoritative source for optional BAM tags?
duplicates picard markduplicates bam written 2.6 years ago by John ♦ 12k • updated 9 days ago by RamRS ♦ 17k
6
votes
1
answer
178
views
1
answer
How to interpret the "Matrics" file of MarkDuplicates (Picard)
picard markduplicates written 26 days ago by ravipatel4 • 10
2
votes
1
answer
161
views
1
answer
GATK MarkDuplicates output and bam
gatk markduplicates written 6 weeks ago by cmccabe • 170 • updated 6 weeks ago by finswimmer ♦ 5.4k
3
votes
1
answer
205
views
1
answer
Mark duplicates PICARD error: Unable to access jarfile 'MarkDuplicates.jar' with commandline/with R dupRadar package
picard markduplicates rna-seq written 11 weeks ago by salamandra • 170
0
votes
2
answers
278
views
2
answers
Picard MarkDuplicates flag vs remove issue
duplicates picard atac-seq markduplicates written 3 months ago by s1469060 • 10 • updated 3 months ago by prakash • 480
2
votes
1
answer
591
views
1
answer
Picard Mark Duplicates
picard markduplicates written 5 months ago by Varun Gupta • 1.0k • updated 3 months ago by marcela.uliano • 50
2
votes
1
answer
344
views
1
answer
Picard MarkDuplicates fatal error
picard markduplicates written 6 months ago by fwuffy • 50 • updated 6 months ago by h.mon ♦ 19k
5
votes
1
answer
2.9k
views
1
answer
Gatk Pipeline: Markduplicates At The End ?
workflow next-gen pipeline gatk markduplicates duplicates bam written 5.9 years ago by Pierre Lindenbaum ♦ 112k • updated 11 months ago by Biostar ♦♦ 20
1
vote
1
answer
2.1k
views
1
answer
Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
duplicates picard markduplicates bam written 6.0 years ago by ian.streeter • 10 • updated 15 months ago by Biostar ♦♦ 20
2
votes
1
answer
933
views
1
answer
Split the bam file by chromosome and speed up picard Markduplicates
next-gen alignment markduplicates sequencing written 16 months ago by lghust2011 • 80 • updated 16 months ago by Pierre Lindenbaum ♦ 112k
3
votes
0
answers
678
views
0
answers
picard MarkDuplicates find EOF problem
eof markduplicates written 16 months ago by victoria_aleks • 30
0
votes
1
answer
562
views
1
answer
Questions about LB field in SAM specification for PCR duplicate removal
sam markduplicates written 17 months ago by James Ashmore • 2.5k
1
vote
0
answers
713
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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 18 months ago by pentiumy • 10 • updated 18 months ago by Pierre Lindenbaum ♦ 112k
1
vote
1
answer
1.2k
views
1
answer
Error in picard tool: Mark Duplicates
software error sam-input picard markduplicates written 19 months ago by jcanitz • 0 • updated 19 months ago by dariober ♦ 9.4k
3
votes
0
answers
795
views
0
answers
Picard MarkDuplicates stuck at Traversing read pair information and detecting duplicates
picard markduplicates bam written 20 months ago by 14134125465346445 • 3.4k
3
votes
1
answer
1.8k
views
1
answer
Picard Markduplicates output
next-gen picard markduplicates written 2.3 years ago by VasGene • 10 • updated 2.3 years ago by Amitm • 1.6k
0
votes
2
answers
2.8k
views
2
answers
Picard MarkDuplicates error: Value was put into PairInfoMap more than once
bedtools picard samtools markduplicates written 2.6 years ago by nbhardwaj • 110 • updated 2.4 years ago by Peter Georgeson • 0
4
votes
1
answer
1.8k
views
1
answer
Problem using PicardTools MarkDuplicates: Value Was Put Into Pairinfomap More Than Once
pairinfomap picard picardtools markduplicates written 2.5 years ago by anp375 • 140 • updated 2.5 years ago by Matt Shirley ♦ 8.6k
1
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0
answers
3.0k
views
0
answers
MarkDuplicates memory issue
alignment picard markduplicates written 2.7 years ago by cacampbell • 40
2
votes
2
answers
2.6k
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2
answers
Mark duplicates for single end reads: Why only 5'end?
read duplicates 5' 3'end markduplicates written 3.4 years ago by dariober ♦ 9.4k
4
votes
0
answers
1.1k
views
0
answers
Is there software that takes advantage of MarkedDuplicates for SNP calling?
gatk markduplicates snp consensus sequence written 3.4 years ago by shuelga • 20
16
votes
4
answers
2.5k
views
14 follow
4
answers
sam/bam file handling -> new tools?
bam sort markduplicates sam written 3.5 years ago by Richard • 550 • updated 3.5 years ago by lh3 ♦ 31k
2
votes
1
answer
1.7k
views
1
answer
How does samblaster use library tag information if at all?
markduplicates samblaster written 3.9 years ago by Carlos Borroto • 1.7k • updated 3.6 years ago by gf4ea • 30
9
votes
1
answer
4.4k
views
5 follow
1
answer
Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
picard samtools markduplicates bam sort written 4.4 years ago by Jordan • 1.0k • updated 3.8 years ago by 1013002214 • 0
9
votes
2
answers
10k
views
2
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Markduplicates: Value Was Put Into Pairinfomap More Than Once
picard markduplicates written 5.7 years ago by lifuqiang0611 • 20 • updated 3.8 years ago by karl.stamm ♦ 3.3k
5
votes
2
answers
2.2k
views
2
answers
markDuplicates: Histogram not produced
picard markduplicates written 4.0 years ago by dariober ♦ 9.4k
5
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1
answer
3.3k
views
1
answer
Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does not equal value computed..."
picard markduplicates sam validation error written 4.1 years ago by Mark Ebbert • 70 • updated 4.1 years ago by lomereiter • 420
13
votes
3
answers
2.9k
views
7 follow
3
answers
Tool to unmark duplicates
picardtools samtools markduplicates pcr duplicates written 4.2 years ago by Mark Ebbert • 70 • updated 4.2 years ago by Pierre Lindenbaum ♦ 112k
10
votes
1
answer
4.8k
views
1
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Picard MarkDuplicates and SamTools rmdup algorithm documentation
picard samtools markduplicates rmdup written 4.2 years ago by Mark Ebbert • 70 • updated 4.2 years ago by Pierre Lindenbaum ♦ 112k
9
votes
1
answer
2.2k
views
1
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Will Picard MarkDuplicates also un-mark duplicates?
duplicates ngs picard markduplicates bam written 4.3 years ago by Chris Miller ♦ 20k • updated 4.3 years ago by Pierre Lindenbaum ♦ 112k
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