mozack abra2 issues - Githubissues

mozack / abra2

ABRA2

MIT License

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issues

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Window size vs targets - using targets only?

#62 ranasats opened 1 week ago
3
Abra2-processed bams are incompatible with Strelka2

#61 lculibrk opened 7 months ago
0
Specific case that ABRA2 is not realigning correctly

#60 parsaeskandar opened 9 months ago
0
IndelRealigner-parameters vs Abra2-parameters

#59 Manuel-DominguezCBG opened 1 year ago
1
How to shorten run time

#58 jingjing578 opened 1 year ago
4
build fails on linux

#57 yangxingyu588 opened 1 year ago
0
Unknown format conversion exception

#56 abhiku0007 opened 1 year ago
1
Fusions

#55 gitMakeCoffee opened 1 year ago
0
Abra2 creating large (around 100bp) deletions to alignment

#54 rchapman2000 opened 1 year ago
0
Bump htsjdk from 2.8.1 to 3.0.1

#53 dependabot[bot] opened 2 years ago
0
java.lang.OutOfMemoryError: Java heap space

#52 AdilyAid opened 2 years ago
1
Abra and log4j

#51 colindaven opened 2 years ago
0
Alternate or duplicate alignment in output

#50 jgaupp-invitae closed 2 years ago
1
Score threshold and content of the printed INFO

#49 camillebenoist opened 3 years ago
0
java.lang.IllegalArgumentException: Invalid reference index -1

#48 ThanosPAS opened 3 years ago
1
Minor update to Readme.md

#47 alanhoyle opened 3 years ago
0
v2.24 gives "Error loading: libAbra.so", older versions do not

#46 chrisamiller opened 3 years ago
7
max_paths_from_root

#45 warthmann opened 3 years ago
3
Num reads to scan for read length/insert length/mapq

#44 danoreper opened 3 years ago
0
Bed file format

#43 V-Catherine opened 4 years ago
1
feature request: stdin functionality

#42 eboyden opened 4 years ago
0
workflow of data pre-processing of RNAseq

#41 SaHash closed 4 years ago
6
Realigned output bam TLEN field plus/minus sign when FLAG == 147

#40 Julie-Zhongyun-Huang opened 4 years ago
2
java.lang.IllegalArgumentException: Contig too long

#39 warthmann closed 4 years ago
4
Compilation on Mac

#38 edgardomortiz opened 5 years ago
0
compilation terminated during make

#37 zhoutengsheng opened 5 years ago
3
Identical runs give slightly different results

#36 sfrenk closed 5 years ago
8
glibc2.14

#35 Tjitskedv closed 5 years ago
2
Abra2 output BAM processing

#34 roysomak4 closed 5 years ago
2
Expected memory requirements

#33 ionox0 opened 5 years ago
7
YO tag format

#32 ionox0 closed 5 years ago
6
MD tags for realigned reads

#31 rawagiha closed 5 years ago
4
new reverseComplement implementation

#30 dmcmanam closed 5 years ago
0
Supplementary alignment behavior question

#29 dstreett opened 5 years ago
1
Dockerfile

#28 alanhoyle opened 5 years ago
0
what's wrong with that ref

#27 panxiaoguang closed 5 years ago
1
abra2 break the order of sam file tags.

#26 y9c closed 5 years ago
1
abra2 error java.lang.NumberFormatException

#25 rimzaag opened 5 years ago
4
Option to prevent reads ending with complex indel

#24 jakobmatthes closed 5 years ago
7
JProfiler results show 39.1% time spent in ReverseComplementor.reverseComplement

#23 dmcmanam closed 5 months ago
0
Invalid read written

#22 marc-sturm closed 6 years ago
1
Increase MAX_SAMPLES to 12 or 16

#21 ckandoth closed 6 years ago
2
Using abra/abra2 for local assembly of pacbio reads?

#20 ggstatgen closed 6 years ago
1
Dockerfile for ABRA2

#19 alanhoyle closed 5 years ago
2
crash with java IndexOutOfBoundsException

#18 anso-sertier closed 6 years ago
26
Comparison with GATK's IndelRealigner?

#17 iskandr closed 6 years ago
4
Crash when target region BED file contains header lines

#16 imgag closed 7 years ago
3
Explosion on CIGARS using = and X operators

#15 Lenbok opened 7 years ago
3
IndexOutOfBoundsException at AltContigGenerator.java#L273

#14 hemp closed 7 years ago
2
UnsatisfiedLinkError on Mac OS

#13 Asutu closed 7 years ago
2