GregoryFaust samblaster issues

GregoryFaust / samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

MIT License

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issues

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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