issues
search
hsinnan75
/
MapCaller
MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
30
stars
5
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
BWAmem vs Mapcaller mapping stats
#72
danessel
opened
2 years ago
1
Location of temp files for -r
#71
tseemann
opened
3 years ago
2
-monomorphic missing DP=0 sites?
#70
tseemann
opened
3 years ago
0
Need -label for sample ID in VCF output
#69
tseemann
closed
3 years ago
2
Invalid GT in Gaps
#68
tseemann
opened
3 years ago
2
VCF 'Gaps' line has wrong REF base / coordinate
#67
tseemann
opened
3 years ago
3
Missing \n in VCF header
#66
tseemann
opened
3 years ago
1
Can you move to htslib 1.11 ?
#65
tseemann
closed
3 years ago
2
Wrong case in VCF file - REF vs Ref and missing q10
#64
tseemann
closed
3 years ago
2
Gaps END is 1 bp too long?
#63
tseemann
closed
4 years ago
12
Typo in -help
#62
tseemann
opened
4 years ago
0
Alignment in homopolymer regions
#61
tseemann
opened
4 years ago
6
Corrupt BAM files being produced in 0.9.9.37
#60
tseemann
closed
4 years ago
1
[W::sam_parse1] mapped mate cannot have zero coordinate; treated as unmapped
#59
tseemann
opened
4 years ago
1
What are the magic numbers 0.25 and 0.35 in the source code?
#58
tseemann
opened
4 years ago
3
Empty genotype GT for some indels ?
#57
tseemann
closed
4 years ago
3
Gaps seem to be too big?
#56
tseemann
closed
4 years ago
6
Unknow parameter: -min_cnv
#55
tseemann
closed
4 years ago
3
##reference=tmp_idx
#54
tseemann
closed
4 years ago
2
Sort BAM by coordinate not name?
#53
tseemann
closed
4 years ago
2
Does `-bam -` send the BAM to stdout ?
#52
tseemann
closed
4 years ago
5
Meaning of DUP in vcf output
#51
tseemann
opened
4 years ago
3
Behaviour scaling to more threads
#50
tseemann
closed
4 years ago
6
Different mapping with different -t threads ?
#49
tseemann
opened
4 years ago
3
Automatic index of a FASTA file reference
#48
tseemann
closed
4 years ago
3
Put bwt_index into MapCaller -idx ?
#47
tseemann
closed
4 years ago
3
Report average read length in statistics?
#46
tseemann
closed
4 years ago
3
Typos in information field and header
#45
qhelleu
closed
4 years ago
2
add summary option
#44
fei0810
closed
4 years ago
3
Incorrect definition of VCF header
#43
motthy
closed
4 years ago
2
Fix typo on Devon's name
#42
tseemann
closed
4 years ago
0
vcf convert plink format
#41
feng0377
closed
4 years ago
4
Compilation error
#40
dpryan79
closed
4 years ago
5
REF prefixes differ for indels across vcfs
#39
qhelleu
closed
4 years ago
8
How are ambiguous bases in reads (or reference) handled?
#38
tseemann
opened
4 years ago
5
Getting nucleotide counts at each position
#37
tseemann
closed
4 years ago
6
How do i only accept (mostly) glocal alignments?
#36
tseemann
closed
4 years ago
6
How does MapCaller handle multiple mapping?
#35
tseemann
closed
4 years ago
8
Typo `Allele depth`
#34
tseemann
closed
4 years ago
1
Add installation instructions for brew and conda
#33
tseemann
closed
4 years ago
1
VCF headers missing 3 things
#32
tseemann
closed
4 years ago
2
Difference betweek -alg ksw2 and nw
#31
tseemann
closed
4 years ago
3
-ploidy 1 still has diploid genotypes
#30
tseemann
closed
4 years ago
4
Problems with new version numbers
#29
tseemann
closed
4 years ago
1
Large deletion not called
#28
carlosmag
closed
4 years ago
9
starts with bam file
#27
huangl07
opened
4 years ago
5
merge gvcf files
#26
huangl07
opened
4 years ago
10
Strand and read placement biases
#25
carlosmag
opened
4 years ago
4
Include monomorphic sites in VCF
#24
carlosmag
opened
4 years ago
13
Duplicated reads handling
#23
carlosmag
opened
4 years ago
11
Next