PapenfussLab/gridss

Issues

• ALT coordinate

  #685 opened 11 days ago by uretaj
  1

• Conda install doesnt work

  #684 opened a month ago by amcpherson
  0

• Joint assembly and calling for multiple tumor/normal sample pairs

  #683 opened a month ago by ypradat
  1

• gridss results MERGE problems with other SV recognition software

  #672 opened 3 months ago by HuangYihang1222
  3

• No index

  #681 opened 2 months ago by ucsfpan
  0

• Are the docker image GRIDSS2 or GRIDSS version 1?

  #682 opened 2 months ago by lwtan90
  0

• Running into errors with conda version while docker/singularity work fine

  #676 opened 3 months ago by famosab
  2

• What is the exact command to run gridss_somatic_filter?

  #680 opened 2 months ago by lwtan90
  0

• Structural Variation Identification Using GRIDSS

  #679 opened 2 months ago by anitha-ravichandran
  0

• Are dependencies included in the docker image?

  #678 opened 3 months ago by lwtan90
  1

• Illegal seek

  #677 opened 3 months ago by avrajit
  2

• Fatal error: missing assembly is not missing

  #674 opened 3 months ago by afurches
  0

• ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 1-15215340, Mate Alignment start should be 0 because reference name = *

  #675 opened 3 months ago by kuangzhuoran
  0

• SoftClipsToSplitReads error: mem: invalid option -- 'K'

  #673 opened 3 months ago by kostasgalexiou
  0

• NullPointerException during CollectGridssMetricsAndExtractSVReads

  #671 opened 3 months ago by vrohnie
  0

• How to find out INV?

  #670 opened 3 months ago by jamesc99
  1

• Docker img doesnt work

  #669 opened 3 months ago by saphir746
  0

• Unrecognized option: -r

  #668 opened 4 months ago by gamzemdn
  3

• Running Joint Calling

  #667 opened 4 months ago by HenryMarshall97
  0

• bcftools have no mpileup

  #665 opened 4 months ago by lqsae
  0

• VIRUSBreakend does not work

  #666 opened 4 months ago by lqsae
  1

• Clarify `--assembly` in documentation

  #664 opened 5 months ago by famosab
  0

• Error with `gridss_somatic_filter`

  #663 opened 5 months ago by Teezi
  2

• Advice needed in regards to the GRIDSS blacklist

  #662 opened 5 months ago by Teezi
  0

• SVTYPE is Deprecated in Variant Call Format Specification

  #661 opened 6 months ago by DarioS
  3

• error with simple-event-annotation.R script

  #656 opened 8 months ago by shaghayeghsoudi
  2

• Questions about using virusbreakend

  #657 opened 6 months ago by joaohl216
  1

• Difference in number of integrations in virus summary vs. VCF

  #658 opened 6 months ago by AqsaAlam
  3

• Indexed block-compressed FASTA file cannot be handled

  #659 opened 6 months ago by keeblee
  2

• Input BAM not recognized

  #653 opened 6 months ago by espelpz
  1

• RNA support

  #654 opened 6 months ago by kesner
  1

• how to filter breadends that are only present in particular samples?

  #660 opened 6 months ago by yqlan
  1

• Unable to run GRIDSS jar

  #652 opened 10 months ago by vialimju
  3

• VIRUSBREAKEND > failure identifying viral sequences

  #644 opened a year ago by josh11351
  2

• about VIRUSBREAKEND output

  #655 opened 9 months ago by hidehitofukushima
  0

• Can't retrieve reference files for GRIDSS-Purple-Linx pipeline

  #650 opened a year ago by pbousquets
  0

• GRIDDS results benchmarking queries:

  #649 opened a year ago by poddarharsh15
  2

• Assemble step error

  #648 opened a year ago by poddarharsh15
  5

• Error when running gridss_somatic_filter

  #635 opened a year ago by kcleal
  8

• PoN: bed & bedpe

  #647 opened a year ago by acarbome7
  1

• GRIDSS AnnotateInsertedSequence error with ~2.8 million SV events: htsjdk.samtools.util.RuntimeIOException: Stream closed

  #646 opened a year ago by scwatts
  0

• How to deal with bwa index and bowtie2 bam files?

  #645 opened a year ago by Ceonham
  0

• singularity, error on creating temp files

  #643 opened a year ago by aheravi
  0

• Blacklist errror

  #642 opened a year ago by uretaj
  1

• Exit code 9 when using hs37d5

  #641 opened a year ago by uretaj
  2

• Can gridss be used to mouse genome?

  #640 opened a year ago by Kailiang-Qiao
  1

• Disable pdf creation/running R scripts at preprocess step

  #638 opened a year ago by pruzanov
  0

• virusbreakend docker image issue: BAM index not found

  #639 opened a year ago by ugh-astya
  0

• T2T reference

  #637 opened a year ago by BethHudson-Lund
  1

• gridss for long-read data?

  #636 opened a year ago by kerstinth
  2