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196 Open 113 Closed
196 Open 113 Closed
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Issues list

Non-text characters appearing in SEQ field
#402 opened Sep 6, 2023 by csoeder
How to interpret the meaning of flag=0 in the alignment results of BAM files generated by bwa-mem2 mem
#400 opened Sep 1, 2023 by wlhCNU
Is this an wrong alignment score in bwa-mem alignment?
#398 opened Aug 15, 2023 by huichanghuang
[mem] reads are not labelled as proper pair
#397 opened Aug 7, 2023 by ftian9
clipping penalty
#396 opened Jun 23, 2023 by FarGlasgow
bwa aln -m maximum entries in the queue not documented in manual
#394 opened Jun 7, 2023 by marykthompson
BWA BAM
#393 opened May 16, 2023 by duhuipeng
3
xa2multi.pl outputs RNEXT w.r.t. original alignment
#390 opened Apr 26, 2023 by tsnorri
1
1
Can I use Apache2 branch under Apache 2.0 license?
#389 opened Mar 29, 2023 by pasang0000
question on mapping to short reference like 1kb
#388 opened Feb 14, 2023 by jianshu93
bwa mem failed to locate index files
#386 opened Feb 8, 2023 by isabelluo
1
Extracting read pairs that have been concordantly aligned exactly 1 time
#384 opened Jan 27, 2023 by poecile-palustris
run-gen-ref
#383 opened Jan 24, 2023 by StefanoLise
bwa mem -a and -t options are incompatible?
#382 opened Jan 3, 2023 by yazhinia
mapping on subset of a bigger reference gives different results
#381 opened Jan 3, 2023 by mewu3
A error ouput for bwa mem
#380 opened Nov 26, 2022 by fengchuiguo1994
Multimapping and reference sequence junctions
#379 opened Nov 1, 2022 by s-a-nersisyan
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
#378 opened Oct 30, 2022 by crispychilli
bwa mem -a output all alignments for SE or unpaired PE
#377 opened Oct 27, 2022 by fanshu1986
1
bwa mem or bwa sw
#376 opened Oct 13, 2022 by Oksanak22
re compiling bwa on mac (M1)
#374 opened Sep 29, 2022 by haircell
2
The official full names of "bntseq", "bntann", "bntamb", "bns".
#373 opened Sep 9, 2022 by mathgirl796
Number of characters per line for a reference sequence
#372 opened Sep 7, 2022 by olu2016
Add HLA-DPB1 typing
#368 opened Aug 12, 2022 by Gerde
add break condition to making cigar string
#366 opened Aug 5, 2022 by gayoung-MetisX
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