hsinnan75 MapCaller issues

hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

MIT License

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issues

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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