Illumina/manta

Issues

• Failed to complete command task: 'generateCandidateSV_0000', error code: 1

  #235 opened 4 years ago by Boer223
  7

• [generateCandidateSV_0000] [E::hts_open_format] Failed to open file

  #220 opened 5 years ago by moahaegglund
  2

• Reference genome mismatch: Reference fasta file is missing a chromosome found in the Normal BAM/CRAM file: 'ERCC-00002'

  #211 opened 5 years ago by azzatha
  1

• Problems with --callRegions

  #231 opened 4 years ago by anfimoagbr
  1

• Manta cannot detect same chromosome large deletions

  #255 opened 4 years ago by jdzdroid
  7

• Permission Denied Error with convertInversion.py

  #248 opened 4 years ago by mdbjax
  2

• "ulimit -s unlimited" but got "Too many open files"

  #245 opened 4 years ago by lindenb
  3

• Finished install but can't run the demo

  #251 opened 4 years ago by eeleclair
  2

• Manta on Python3

  #233 opened 4 years ago by WKabza
  3

• Manta output merging

  #244 opened 4 years ago by nitha26
  1

• germline SV calls: keep only PASS?

  #250 opened 4 years ago by cagaser
  1

• Running Manta with WGS data takes a lot of time

  #213 opened 5 years ago by zhaoxia-genedock
  4

• [ERROR] Failed to complete command task

  #238 opened 4 years ago by AlisaFbb
  1

• Update on genotyping option?

  #247 opened 4 years ago by katherinef
  2

• Manta does not support Python3.6.6 ??

  #256 opened 4 years ago by pkMyt1
  1

• Manta false negative large deletion - finds PR evidence but qual=0

  #259 opened 4 years ago by rhalperin
  0

• 1bp missmatch between BAM and reference genome

  #258 opened 4 years ago by Hywel-W
  0

• false negative with no edges in svLocusGraph?

  #257 opened 4 years ago by rhalperin
  0

• Large Inversion interpretation

  #254 opened 4 years ago by davidvilanova
  0

• Failed to complete command task: 'generateCandidateSV_0000'

  #216 opened 5 years ago by azzatha
  4

• Task status at 'generateCandidateSV_0000'

  #253 opened 4 years ago by Mkddb
  0

• some question about output file candidateSV.vcf.gz

  #252 opened 4 years ago by ChenDepp
  0

• Can't compile without sudo - can't link to libstdc++.a on custom directory

  #249 opened 4 years ago by lferreiraMD
  0

• ERROR: 'mergeLocusGraphInputList'

  #230 opened 4 years ago by AndreHolzer
  1

• estimate data (BAM format) processing time (manta 1.6.0)

  #243 opened 4 years ago by jeffchen2000
  0

• Manta error with EstimateSVLoci on WGS bam

  #242 opened 4 years ago by ramsainanduri
  0

• How to print out SR?

  #241 opened 4 years ago by hhzhongchn
  0

• how to reduce too many result

  #240 opened 4 years ago by QuanLG
  0

• Depth and Allele frequency calculations

  #228 opened 4 years ago by Nitin123-4
  1

• output VCF missing "FORMAT" field?

  #239 opened 4 years ago by cnavery
  0

• Missing variants with high coverage WGS samples. How to capture the missed variants?

  #237 opened 4 years ago by ChristopheLegendre
  0

• Ongoing convertInversion.py issue

  #236 opened 4 years ago by MaximilianStammnitz
  1

• [ERROR] generateCandidateSV_0000 fails with taskExitCode -10

  #234 opened 4 years ago by savalipa
  0

• several sample have a signaficant higher SV numbers among groups

  #232 opened 4 years ago by wanhui5867
  0

• Another " Failed to complete command task: 'generateCandidateSV_0000' "

  #217 opened 5 years ago by Fred-07
  3

• Build failed with internal htslib but succeed with external one

  #229 opened 4 years ago by YuZJLab
  1

• What level BAM should Manta be run on

  #227 opened 4 years ago by icanwinwyz
  2

• influence of BED file on variant results

  #226 opened 4 years ago by djomlaart
  0

• build fail on building htslib on macOS 10.15.4

  #225 opened 4 years ago by Billy-Nie
  0

• Missing mutation in DiploidSV

  #224 opened 5 years ago by rohandavidg
  0

• SEQ='*' error and how to solve it?

  #223 opened 5 years ago by temizna
  0

• python errors running convertInversion.py

  #219 opened 5 years ago by mooreann
  1

• Question about inversion and problem with convertInversion.py script

  #222 opened 5 years ago by ptranvan
  0

• TestAssembler no reference sequence

  #221 opened 5 years ago by fayina
  0

• [generateCandidateSV_0000] ERROR: Failed to close BAM/CRAM file:

  #218 opened 5 years ago by AhmedArslan
  0

• Metric for evaluating the confidence of CNV variants

  #215 opened 5 years ago by HyunjunNam
  0

• ERROR: Manta workflow must be installed prior to running demo

  #214 opened 5 years ago by anupullanhi
  0

• generateCandidateSV taskExitCode -11

  #212 opened 5 years ago by bryce-turner
  2

• SV output from Manta - unknown symbol for variant type

  #210 opened 5 years ago by azlinIMR
  0

• SVs shared by tumor and normal samples

  #209 opened 5 years ago by ivanbelzen
  0