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blachlylab
/
fade
Fragmentase Artifact Detection and Elimination
MIT License
11
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Non-printable characters in ab:Z field
#33
divonlan
opened
1 year ago
3
PF variants in fade region are not totally filtered
#32
xiucz
opened
2 years ago
2
Warning or error log in fade annotate ?
#31
xiucz
closed
2 years ago
2
fade stats-clip output documentation?
#30
jon-nowacki
opened
2 years ago
1
negative values for 'read count', 'Clipped %', etc
#29
rhalperin
opened
2 years ago
1
fade out -c fails or produces truncated bam
#28
rhalperin
closed
2 years ago
4
fade missing many reads that appear to be fragmentation artifacts
#27
rhalperin
opened
2 years ago
18
fade out runs extremely slow on a name sorted bam
#26
rhalperin
closed
2 years ago
5
error running fad stats
#25
rhalperin
closed
2 years ago
7
Docker: Use mimalloc
#24
charlesgregory
closed
2 years ago
0
Need unittests
#23
charlesgregory
opened
2 years ago
0
Exception when adding the bam tag.
#22
yangyxt
closed
2 years ago
7
invalid pointer issue
#21
yangyxt
closed
2 years ago
13
Switch for turning on Fade filtering
#20
Kekananen
closed
3 years ago
2
ab:z tag conflicting with samfile format
#19
kristin-watchmaker
closed
3 years ago
12
Bam sorting
#18
charlesgregory
closed
3 years ago
1
Upgrade to dhtslib 1.11
#17
charlesgregory
closed
3 years ago
2
How to process mutect2 caller after fade out
#16
deb0612
closed
3 years ago
7
Where to run in GATK workflow
#15
sowalsky
closed
3 years ago
2
cannot index output file
#14
sinhaeti
closed
3 years ago
2
Question about your use of D
#13
aberba
closed
4 years ago
3
[W::dhtslib.tagvalue.TagValue.this] SA doesn't exist for this record & rs doesn't exist for this record
#12
ShenWei-wei
closed
4 years ago
4
Better help messages
#11
charlesgregory
closed
4 years ago
1
Write shortform statistics to file not stdout
#10
charlesgregory
opened
5 years ago
0
Add option to write out realignments in artifact bam file
#9
charlesgregory
closed
4 years ago
0
Add "release" with build artifacts
#8
jblachly
closed
2 years ago
0
Option to read from stdin and write to stdout
#7
charlesgregory
closed
4 years ago
1
Record artifact alignments
#6
charlesgregory
closed
5 years ago
1
Demo set needed
#5
charlesgregory
opened
5 years ago
0
Documentation needed
#4
charlesgregory
closed
4 years ago
0
Better estimate on mate region size
#3
charlesgregory
closed
5 years ago
1
Migrate to dhtslib fully
#2
charlesgregory
closed
5 years ago
0
Need PG tag in BAM header
#1
jblachly
closed
3 years ago
0