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GregoryFaust
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samblaster
samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
MIT License
220
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30
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de-duplicating a large sam file
#59
morien
opened
1 month ago
2
Can't find first and/or second of pair in sam block of length
#58
CaroleBelliardo
opened
1 year ago
1
Aligning in Biscuit with samblaster and samtools
#57
KChadwick78
opened
1 year ago
1
how do samblaster define a split read?
#56
WZo0o
closed
1 year ago
2
Duplicates were removed but log says 0 dups removed
#55
sehawk
opened
1 year ago
1
Pipe output to samblaster from bwa-mem2
#54
Talo07
closed
3 years ago
1
add support for read group and PCR free optitical duplicate only filtering
#53
carsonhh
opened
3 years ago
0
Please adapt the metrics
#52
ToVste
opened
3 years ago
0
Option to remove split and disc alignments?
#51
biobenkj
opened
3 years ago
1
unmated reads
#50
ghost
closed
3 years ago
1
Alpine-based docker build fails
#49
felixfrenkel
opened
3 years ago
1
walltime is twice cpu seconds
#48
jsmedmar
opened
3 years ago
3
can samblaster tackle reads with UMI?
#47
windtalker6
opened
3 years ago
1
Very different result between samtools and samblaster
#46
biozzq
closed
4 years ago
3
Can't find first and/or second of pair error
#45
dheerajbobbili1988
opened
4 years ago
1
Avoid warning about missing space around literal
#44
marcelm
closed
4 years ago
1
Segmentation fault on getting split reads from long read file?
#43
cmdcolin
closed
4 years ago
7
Getting splitters BAM from long reads data?
#42
cmdcolin
closed
4 years ago
7
Duplicate `MC` tags in samblaster output
#41
DonFreed
closed
4 years ago
6
remove duplicate for single-end read
#40
timedreamer
closed
4 years ago
4
Can not run MarkDup for very large bam file
#39
liujiayi771
closed
5 years ago
1
Support for DT tag to distinguish PCR and optical duplicates
#38
seboyden
opened
5 years ago
6
Can't find first and/or second of pair in sam block of length 1 for id:...
#37
bibbers93
closed
4 years ago
3
threading
#36
ttriche
closed
6 years ago
5
Filter out soft/hard clipped reads in a pipe SAM -> SAM ?
#35
tseemann
opened
6 years ago
5
split reads detection parameters
#34
alantsangmb
closed
6 years ago
1
spitters : I don't get understand the code :-)
#33
lindenb
closed
6 years ago
1
Is samblaster readgroup aware?
#32
crazyhottommy
closed
6 years ago
4
discordant read pairs and split reads
#31
WortJohn
closed
7 years ago
1
Read pair detection failure from biscuit-aligned reads
#30
tantrev
closed
4 years ago
6
Fix broken headings in Markdown files
#29
bryant1410
closed
6 years ago
0
output file option segmentation fault
#28
mken418
closed
7 years ago
1
Question about "A read-id grouped SAM file"
#27
jiadong324
closed
7 years ago
2
segfault during hashTableInsert
#26
chapmanb
closed
7 years ago
3
Plans to use htslib ?
#25
tseemann
closed
7 years ago
2
Don't add MC and MQ tags to a read if its mate is unmapped
#24
ernfrid
closed
7 years ago
1
Handle chrM discordants differently
#23
jdidion
opened
8 years ago
0
More info for missing pair
#22
zeeev
closed
7 years ago
4
non-human genomes with many contigs
#21
carsonhh
closed
7 years ago
5
Support for UMIs
#20
mjafin
opened
8 years ago
6
Too many sequences in header of input sam file
#19
vladimirkovacevic
closed
8 years ago
7
after extracting disc and split reads, does the final bam still contain them?
#18
crazyhottommy
closed
8 years ago
1
added -m/-metricsFile flag to output duplication metrics
#17
dakl
closed
4 years ago
6
Write duplication metrics to file
#16
dakl
closed
4 years ago
2
workaround for bam files with some singleton reads
#15
elzbth
closed
9 years ago
6
Makefile error OS X
#14
LeahRoberts
closed
9 years ago
2
Avoid buffer length issues when marking long SAM lines
#13
chapmanb
closed
9 years ago
2
Mate tags
#12
cc2qe
closed
9 years ago
1
Support multiple clipping operations at the beginning of a read
#11
ernfrid
closed
9 years ago
3
Add support for N opcode
#10
holtgrewe
closed
9 years ago
5
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