lh3 bwa issues - Githubissues

lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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Add UR field to SQ line in SAM output

#236 marchoeppner closed 5 years ago
2
Some Alignments Have Impossible Flag Values

#235 DarioS opened 5 years ago
1
Insert Penality Not An Option

#234 DarioS closed 5 years ago
1
0.7.17 precompiled binary for Linux

#233 zeus19900814 closed 5 years ago
2
Buffer overflow while storing .alt file using bwa mem

#232 zachbthomas closed 5 years ago
0
How to create .alt index file?

#231 hp2048 closed 5 years ago
10
bwasw extremely slow on plant genomes

#230 maximilianh opened 5 years ago
11
bwa 0.7.17-r1188 on intel e3 cpu

#229 penguims opened 5 years ago
0
Paired reads have different names

#228 MichaelVirology opened 5 years ago
13
fix incorrect secondary alignment in ksw_align

#227 mirounga opened 5 years ago
0
bwa mem 20% speedup with vector instructions (Fixed intel-extend branch)

#226 zamaudio opened 6 years ago
1
bwa-mem aligned reads into a gap

#225 zhangrengang opened 6 years ago
0
ENH: add SA calculation to example.c

#224 brentp opened 6 years ago
0
Randomly assign multiply mapped reads

#223 Jonathan-Abrahams closed 6 years ago
3
Incorrect report of mapped reference name for short reads.

#222 kingdynasty opened 6 years ago
2
speed up alignment by increase index file size?

#221 jia-zhuang opened 6 years ago
0
bwa-postalt.js Allocation error - process out of memory

#220 jbird361 closed 6 years ago
0
failed to make

#219 kemin711 closed 5 years ago
1
How can I used *.fa.bwt in my own script

#218 loganylchen opened 6 years ago
0
k == 0 causes out-of-bound access

#217 ycgasjy closed 6 years ago
1
seg fault on a specific read pair

#216 sb10 closed 6 years ago
1
unmapped read pair

#215 xtmgah opened 6 years ago
0
softclipping query

#214 prasundutta87 closed 6 years ago
2
Mapping quality cap

#213 dancooke closed 6 years ago
8
Fix typo: Malformated → Malformed

#212 tskir opened 6 years ago
0
NH tag

#211 apredeus opened 6 years ago
4
The reads rank in fq.gz influence the MAPPING results?

#210 loganylchen opened 6 years ago
0
How to get the randomly best hit with bwa-mem?

#209 zhangrengang opened 6 years ago
0
bwa mem - memory usage with paired reads vs single reads

#208 unode opened 6 years ago
0
Rebased intel-extend branch - 10% speedup using SSE4 (AVX2 even faster)

#207 zamaudio closed 6 years ago
1
bwa mem -a option

#206 prasundutta87 opened 6 years ago
0
Error handling of empty sequence

#205 caleblareau opened 6 years ago
0
Bwa ONT parameters

#204 npavlovikj opened 6 years ago
0
Add -C param for sampe/samse, to copy fastq comments into sam output

#203 grahamgower opened 6 years ago
0
Implement -v/--version option

#202 fbartusch closed 5 years ago
2
How is isize calculated for PE reads?

#201 sfchen closed 6 years ago
1
EOF marker is absent. The input is probably truncated.[bam_header_read] invalid BAM binary header (this is not a BAM file)

#200 U201412486 opened 6 years ago
0
Patch proposals for interactively working with BWA

#199 nh13 opened 6 years ago
0
Proposed enhancement to the FAQ with a line for -M

#198 mdkeehan opened 6 years ago
2
Error: /usr/bin/ld: cannot find -lz

#197 rakesh4osdd opened 6 years ago
0
Sai file was created but having 0 size

#196 kimdh27 opened 6 years ago
0
argument order

#195 outpaddling closed 6 years ago
2
position inconsistent with reference length

#194 rwhetten closed 6 years ago
1
Testing practices

#193 ionox0 opened 6 years ago
0
shuffling reads leads to different outputs

#192 agrippa closed 6 years ago
1
How can I get the exact match?

#191 jia-zhuang opened 6 years ago
1
Bug/patch: bwa-postalt.js writes invalid output for SAM input that is an exact multiple of 65536 bytes in length

#190 ihaque-freenome closed 6 years ago
3
Update bwakit release

#189 godotgildor opened 6 years ago
1
Please enhance documentation on the recommended use of the BWA MEM -M and -Y option

#188 mdkeehan opened 6 years ago
5
Minimum score threshold (`-T` option) is not applied to paired reads

#187 gmagoon opened 6 years ago
5

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