Illumina/paragraph

Issues

• error reference_sequence.empty

  #46 opened 4 years ago by KamilSJaron
  12

• Tool to use for SV clustering that is compatible with paragraph genotyping

  #87 opened 2 months ago by JoannaTan
  0

• When I used the vcf file generated by sniffles to genotyping the ngs data, I got an error like this

  #86 opened 2 months ago by mebius-S
  0

• Distance between vcf position and chrom start is smaller than read length.

  #38 opened 5 years ago by MaoYafei
  3

• Whole Exome Data?

  #85 opened 5 months ago by bbimber
  0

• BAM header only has a subset of the reference chromosomes -- please make sure they match!

  #84 opened 6 months ago by pingxinxing
  0

• Distance between vcf position and chrom start is smaller than read length.

  #83 opened 6 months ago by pingxinxing
  0

• Errors on idxdepth

  #60 opened 4 years ago by Yexin-Zhang
  4

• [BUG] Error adding alt from insertion sequence representing a duplication

  #82 opened 9 months ago by rickymagner
  0

• Problem starting the script multigrmpy.py

  #77 opened 2 years ago by aaaniich
  2

• Format error in vcf line:

  #81 opened a year ago by mrwangyz
  3

• Exception: Different padding base for REF and ALT

  #61 opened 4 years ago by srbehera
  6

• Issue's with Native Build and Boost

  #80 opened a year ago by david2905
  0

• idxdepth error

  #49 opened 4 years ago by biozzq
  3

• Add support for VCFv4.2 breakend notation

  #79 opened 2 years ago by nvnieuwk
  0

• Error when working with `--ins-info-key`

  #78 opened 2 years ago by nvnieuwk
  1

• idxdepth regex option not working

  #76 opened 2 years ago by weilu1998
  0

• Pysam error

  #40 opened 4 years ago by jjfarrell
  6

• Genotyping for SNP

  #75 opened 2 years ago by Wangchangsh
  0

• Stop using Werror and Wall

  #74 opened 2 years ago by dpryan79
  0

• Install paragraph

  #73 opened 3 years ago by vanhoan310
  0

• [E::idx_find_and_load] Could not retrieve index file

  #59 opened 4 years ago by Xuelei-Dai
  7

• no BGZF EOF marker

  #72 opened 3 years ago by xuefenfei712
  0

• Missing key {ins_info_key} for <INS> at {self.chrom}:{vcf.pos};

  #45 opened 5 years ago by Parsoa
  1

• How to merge multi-samples SVs and obtain breakpoints for genotyping a population

  #71 opened 3 years ago by Zhiliang-Zhang
  0

• subprocess.CalledProcessError

  #67 opened 3 years ago by duzezhen
  2

• index file

  #69 opened 3 years ago by MehmetGoktay
  0

• grmpy error: [E::cram_itr_query]

  #68 opened 3 years ago by jasonbhn
  0

• --vcf-split option with no description

  #66 opened 3 years ago by shangshanzhizhe
  0

• Missing key SEQ for <INS>

  #65 opened 4 years ago by brentp
  6

• Error with idxdepth: "Assertion failed: _impl->header_contig_map.count(chr) != 0"

  #64 opened 4 years ago by cassisnaro
  1

• Pysam error message after paragraph genotyping completes

  #57 opened 4 years ago by mchowdh200
  2

• Handling of temporary files by multigrmpy.py

  #54 opened 4 years ago by malemay
  2

• Genotyping unresolved insertions using reads around the breakpoint

  #53 opened 4 years ago by malmarri
  1

• Using more than one input VCF file

  #47 opened 4 years ago by martinghunt
  1

• How to better call and genotype population SVs?

  #52 opened 4 years ago by biozzq
  4

• Compatibility of paragraph and Sniffles VCF

  #51 opened 4 years ago by biozzq
  4

• Error processing an INV

  #43 opened 4 years ago by jjfarrell
  6

• ValueError: Invalid VariantRecord. Number of samples does not match header

  #63 opened 4 years ago by YPGG1234
  2

• Can paragraph be used for indel from 2 bp to 30 bp?

  #62 opened 4 years ago by 349539427
  1

• Which aligner?

  #56 opened 4 years ago by fergsc
  2

• How to reuse variants converted from vcf to json for population genotyping?

  #58 opened 4 years ago by malemay
  0

• Trouble genotyping lifted variants

  #55 opened 4 years ago by Parsoa
  2

• SV calling and genotyping across a population

  #50 opened 4 years ago by biozzq
  2

• Errors when make

  #48 opened 5 years ago by heyaoxi
  2

• Stripping END tag in INFO field

  #44 opened 5 years ago by WEClarke
  3

• Compatibility of paragraph and manta

  #42 opened 5 years ago by KamilSJaron
  13

• INS error

  #39 opened 5 years ago by asylvz
  6

• How to prepare vcf file for Duplication & Tandem Duplication?

  #41 opened 5 years ago by Zhiliang-Zhang
  3

• Illegal character in reference sequence (W base and possibly other noncanonical bases)

  #37 opened 5 years ago by dantaki
  2