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amplab
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snap
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
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Extend Alt contigs option to allow mapping to two haplotypes genomes.
#169
ghuls
opened
11 months ago
0
Add option to add FASTQ comment to SAM output.
#168
ghuls
closed
11 months ago
2
SNAP returning different results?
#167
YasirKusay
closed
1 year ago
2
Feature request: name sort output
#166
matthdsm
opened
1 year ago
0
mapping HiC read
#165
yangfangyuan0102
opened
1 year ago
0
Snap crashes during sorting step
#164
matthdsm
closed
1 year ago
15
Compression of intermediate bam file
#163
matthdsm
closed
1 year ago
3
bug (?): unexpected results with enforced interval size greater than default
#162
eboyden
opened
2 years ago
4
feature request: customizable quality threshold for -C
#161
eboyden
closed
1 year ago
6
feature request: update @HD to v1.6 specification and add "GO:query" tag for unsorted output
#160
eboyden
closed
1 year ago
3
feature request: print LB/PL/PU/SM tags only in @RG header line
#159
eboyden
opened
2 years ago
0
Feature request: markduplicate metrics and settings
#158
matthdsm
opened
2 years ago
0
Performance tweaking wrt parallel runs
#157
matthdsm
closed
2 years ago
9
"snap" binary in Quick Start guide
#156
hubgit
closed
1 year ago
2
Settings wrt datatype?
#155
matthdsm
closed
1 year ago
5
Indel calling
#154
kokyriakidis
opened
2 years ago
3
Pin a new release
#153
matthdsm
closed
2 years ago
2
Supplementary mappings
#152
kcleal
closed
2 years ago
1
Error - Segmentation fault (core dumped)
#151
klamens
closed
1 year ago
6
Is SNAP effective for high error rate long read data such as Nanopore or others?
#150
jsonProgram
closed
2 years ago
2
Documentation says default seed size is 27 but log and help say 24
#149
eboyden
closed
2 years ago
3
-= doesn't work in SAM
#148
bolosky
closed
2 years ago
1
feature request: option to mark optical duplicates only
#147
eboyden
opened
2 years ago
1
feature request: option to move fastq comments to sam tags
#146
eboyden
closed
1 year ago
26
Duplicate marking produces malformed QS tags in SAM output
#145
eboyden
opened
2 years ago
3
sorting doesn't work with SAM output?
#144
eboyden
closed
2 years ago
7
better handling of complex indel situations
#143
bwlang
opened
2 years ago
3
Don't require /1 /2 headers
#142
bwlang
closed
2 years ago
8
Question: Can aligned and unaligned reads be outputted into separate BAMs?
#141
danfulop
closed
2 years ago
0
building index
#140
biolxy
closed
2 years ago
6
Binary for Linux
#139
ksahlin
closed
2 years ago
3
Bad error message for too-long reads
#138
YasirKusay
closed
2 years ago
8
CPU affinity
#137
jkbonfield
closed
2 years ago
2
Sorting error
#136
tylerjkennedy
closed
3 years ago
12
Running SNAP on macOS
#135
tylerjkennedy
closed
3 years ago
9
The two FASTQ files are not the same size!
#134
tylerjkennedy
closed
3 years ago
2
controlling memory usage for sort/index/markdup
#133
teerjk
closed
3 years ago
13
Feature request - accept .fa.gz input files
#132
haiqu
closed
2 years ago
2
-so option seems to sort in reverse order
#131
haiqu
closed
2 years ago
7
Non-x86 support
#130
mr-c
opened
3 years ago
3
segfault: OpenMemoryMappedFile datatest/OverflowTable mmap failed: Invalid argument
#129
mr-c
closed
3 years ago
5
spelling/grammer fixes
#128
mr-c
closed
3 years ago
0
Original fastq order
#127
jkbonfield
opened
4 years ago
2
High number of duplicates with -so option
#126
carlosmag
closed
4 years ago
3
Low % of properly paired reads
#125
carlosmag
closed
4 years ago
10
make error
#124
Ckhyriem
closed
4 years ago
2
Occur Segmentation fault (core dumped) problem
#123
sjlgg
closed
5 years ago
6
Has any version can index fasta file more large than 4.2G？
#122
Winjor
closed
4 years ago
1
Truncated output
#121
ParkvilleData
closed
5 years ago
4
sort issue
#120
jpofmars
closed
4 years ago
2
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