mitoNGS MToolBox issues

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data

http://sourceforge.net/projects/mtoolbox/?source=navbar

GNU General Public License v3.0

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issues

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Error in the "Assembling MT GENOMES WITH assemblemtegenome

#64 Confurious closed 5 years ago
11
error message for vcf output

#63 Pilibeibei opened 6 years ago
1
please update release tags

#62 0xaf1f closed 5 years ago
3
DP4 in the VCF File (enhancement) ?

#61 3i-v closed 5 years ago
3
New issues after update after April 2018

#60 Pilibeibei closed 3 years ago
0
assembleMTgenome.py cannot find reference genomes - keeps using default path

#59 prestonj222 opened 6 years ago
0
Need help with error: no VCF_dict_tmp

#58 dodoflyy opened 6 years ago
2
can MToolBox handle pure mtDNA sequencing data?

#57 dodoflyy closed 5 years ago
1
assembleMTgenome.py error

#56 l0ka closed 5 years ago
1
Unable to successfully run MToolBox using RSRS

#55 l0ka opened 6 years ago
0
MToolBox installing issue Fwd: MToolBox

#54 domenico-simone closed 6 years ago
0
Does MToolBox have been tested on FASTQ coming from the Ion Proton Sequencing Platform ?

#53 3i-v opened 6 years ago
2
GT format in MToolBox VCF to make this compatible with downstream tools

#52 clody23 closed 5 years ago
1
vcf-file format

#51 sboer closed 6 years ago
3
Unable to get .vcf file after finish running MToolBox

#50 tanlingqiao closed 5 years ago
1
Output filename improvement

#49 clody23 closed 6 years ago
0
change rounding of HF

#48 clody23 closed 5 years ago
3
Unable to compute haplogroup. ExitParsing pathogenicity table...

#47 itigupta24 closed 5 years ago
1
mtVariantCaller issue (line 967) | IndexError: string index out of range

#46 3i-v closed 5 years ago
3
Add -o option in install.sh for osx systems

#45 robertopreste closed 7 years ago
1
can MToolBox use stock hg19

#44 EricDeveaud closed 5 years ago
3
GSNAP version update

#43 TakaYamaguchi opened 7 years ago
4
No annotation.csv found.

#42 jich-MCTP opened 7 years ago
5
RSRS vs RCRS

#41 PeggyHXY opened 7 years ago
0
fa file doesnt exist

#40 jeffgreen123 closed 5 years ago
3
Which bam file can be used for IGV view

#39 Pilibeibei closed 5 years ago
1
[mpileup]: IndexError: list index out of range

#38 3i-v closed 7 years ago
14
Out of bounds error

#37 jeffgreen123 opened 7 years ago
3
interpretation of summary file

#36 Pilibeibei opened 7 years ago
0
How or where I can get the file " MITOMAP_HMTDB_known_indels_chrRSRS.vcf"

#35 PeggyHXY closed 7 years ago
3
A question about the HF , homoplasmic and heteroplasmic variant.

#34 hanqingmei closed 5 years ago
4
output file issue when input multiple files

#33 Pilibeibei closed 7 years ago
12
mapExome.py Error

#32 Pilibeibei opened 7 years ago
0
[E::hts_open_format] fail to open file 'OUT.sam.bam' samtools index: failed to open "OUT.sam.bam": No such file or directory

#31 Pilibeibei closed 5 years ago
0
accept also *R1[2]*fastq.gz as input

#30 clody23 opened 7 years ago
0
MToolBox.sh: line 173: check_files.py: command not found

#29 Pilibeibei opened 7 years ago
2
if [ -f OUT_*/*annotation.csv ] -> binary operator expected

#28 3i-v closed 7 years ago
3
multiple annotation.csv files

#27 ma-diroma closed 7 years ago
4
fixed a bug in summary generation

#26 ma-diroma closed 7 years ago
0
normalisation of mtoolbox vcf

#25 clody23 closed 6 years ago
1
No annotation.csv found

#24 3i-v closed 7 years ago
0
fastq.gz input not recognized

#23 Ros85 closed 7 years ago
1
GSNAP MEM usage

#22 clody23 opened 7 years ago
0
mapExome.py in the wrong directory

#21 eturro closed 7 years ago
4
Log file numbering

#20 domenico-simone opened 8 years ago
0
TypeError: unhashable type: 'list'

#19 maojn closed 7 years ago
6
assembleMTgenome.py breaks when sample_name doesn't have an underscore

#18 ghost closed 8 years ago
2
chrM naming issues for rCRS option

#17 ghost closed 8 years ago
2
line 207: `in-out_folders': not a valid identifier

#16 bobbieshaban closed 8 years ago
4
provide proper test file for v1.0

#15 clody23 closed 7 years ago
0

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