illumina/paragraph issues and pull requests

#87 - Tool to use for SV clustering that is compatible with paragraph genotyping

Issue - State: open - Opened by JoannaTan 13 days ago

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

Issue - State: closed - Opened by mebius-S 16 days ago

#85 - Whole Exome Data?

Issue - State: open - Opened by bbimber 4 months ago

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

Issue - State: open - Opened by pingxinxing 5 months ago

#83 - Distance between vcf position and chrom start is smaller than read length.

Issue - State: open - Opened by pingxinxing 5 months ago

#82 - [BUG] Error adding alt from insertion sequence representing a duplication

Issue - State: open - Opened by rickymagner 8 months ago

#81 - Format error in vcf line:

Issue - State: open - Opened by mrwangyz about 1 year ago - 3 comments

#80 - Issue's with Native Build and Boost

Issue - State: open - Opened by david2905 over 1 year ago

#79 - Add support for VCFv4.2 breakend notation

Issue - State: open - Opened by nvnieuwk over 1 year ago

#78 - Error when working with `--ins-info-key`

Issue - State: open - Opened by nvnieuwk over 1 year ago - 1 comment

#77 - Problem starting the script multigrmpy.py

Issue - State: open - Opened by aaaniich almost 2 years ago - 2 comments

#76 - idxdepth regex option not working

Issue - State: closed - Opened by weilu1998 almost 2 years ago

#75 - Genotyping for SNP

Issue - State: open - Opened by Wangchangsh almost 2 years ago

#74 - Stop using Werror and Wall

Issue - State: open - Opened by dpryan79 about 2 years ago

#73 - Install paragraph

Issue - State: open - Opened by vanhoan310 over 2 years ago

#72 - no BGZF EOF marker

Issue - State: open - Opened by xuefenfei712 over 2 years ago

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

Issue - State: open - Opened by Zhiliang-Zhang over 2 years ago

#70 - Added tabix indexing of variants.vcf.gz file

Pull Request - State: open - Opened by ivargr over 2 years ago

#69 - index file

Issue - State: open - Opened by MehmetGoktay about 3 years ago

#68 - grmpy error: [E::cram_itr_query]

Issue - State: open - Opened by jasonbhn about 3 years ago

#67 - subprocess.CalledProcessError

Issue - State: closed - Opened by duzezhen about 3 years ago - 2 comments

#66 - --vcf-split option with no description

Issue - State: open - Opened by shangshanzhizhe over 3 years ago

#65 - Missing key SEQ for <INS>

Issue - State: open - Opened by brentp over 3 years ago - 6 comments

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

Issue - State: open - Opened by cassisnaro over 3 years ago - 1 comment

#63 - ValueError: Invalid VariantRecord. Number of samples does not match header

Issue - State: closed - Opened by YPGG1234 over 3 years ago - 2 comments

#63 - ValueError: Invalid VariantRecord. Number of samples does not match header

Issue - State: closed - Opened by YPGG1234 over 3 years ago - 2 comments

#62 - Can paragraph be used for indel from 2 bp to 30 bp?

Issue - State: open - Opened by 349539427 over 3 years ago - 1 comment

#61 - Exception: Different padding base for REF and ALT

Issue - State: open - Opened by srbehera over 3 years ago - 6 comments

#60 - Errors on idxdepth

Issue - State: open - Opened by Yexin-Zhang over 3 years ago - 4 comments

#59 - [E::idx_find_and_load] Could not retrieve index file

Issue - State: open - Opened by Xuelei-Dai almost 4 years ago - 7 comments

#58 - How to reuse variants converted from vcf to json for population genotyping?

Issue - State: open - Opened by malemay almost 4 years ago

#57 - Pysam error message after paragraph genotyping completes

Issue - State: closed - Opened by mchowdh200 about 4 years ago - 2 comments

#56 - Which aligner?

Issue - State: closed - Opened by fergsc about 4 years ago - 2 comments

#55 - Trouble genotyping lifted variants

Issue - State: closed - Opened by Parsoa about 4 years ago - 2 comments

#54 - Handling of temporary files by multigrmpy.py

Issue - State: closed - Opened by malemay about 4 years ago - 2 comments

#53 - Genotyping unresolved insertions using reads around the breakpoint

Issue - State: closed - Opened by malmarri about 4 years ago - 1 comment

#52 - How to better call and genotype population SVs?

Issue - State: closed - Opened by biozzq over 4 years ago - 4 comments

#51 - Compatibility of paragraph and Sniffles VCF

Issue - State: closed - Opened by biozzq over 4 years ago - 4 comments

#51 - Compatibility of paragraph and Sniffles VCF

Issue - State: closed - Opened by biozzq over 4 years ago - 4 comments

#50 - SV calling and genotyping across a population

Issue - State: closed - Opened by biozzq over 4 years ago - 2 comments

#49 - idxdepth error

Issue - State: closed - Opened by biozzq over 4 years ago - 3 comments

#48 - Errors when make

Issue - State: closed - Opened by heyaoxi over 4 years ago - 2 comments

#47 - Using more than one input VCF file

Issue - State: closed - Opened by martinghunt over 4 years ago - 1 comment

#46 - error reference_sequence.empty

Issue - State: closed - Opened by KamilSJaron over 4 years ago - 12 comments

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

Issue - State: closed - Opened by Parsoa over 4 years ago - 1 comment

#44 - Stripping END tag in INFO field

Issue - State: closed - Opened by WEClarke over 4 years ago - 3 comments

#43 - Error processing an INV

Issue - State: closed - Opened by jjfarrell over 4 years ago - 6 comments

#42 - Compatibility of paragraph and manta

Issue - State: closed - Opened by KamilSJaron over 4 years ago - 13 comments

#41 - How to prepare vcf file for Duplication & Tandem Duplication?

Issue - State: closed - Opened by Zhiliang-Zhang over 4 years ago - 3 comments

#40 - Pysam error

Issue - State: closed - Opened by jjfarrell over 4 years ago - 6 comments

#39 - INS error

Issue - State: closed - Opened by asylvz almost 5 years ago - 6 comments

#38 - Distance between vcf position and chrom start is smaller than read length.

Issue - State: closed - Opened by MaoYafei almost 5 years ago - 3 comments

#37 - Illegal character in reference sequence (W base and possibly other noncanonical bases)

Issue - State: closed - Opened by dantaki about 5 years ago - 2 comments

#36 - Complex structural variants like TRA or INVDUP

Issue - State: closed - Opened by quanc1989 about 5 years ago - 2 comments

#35 - Make filter field for missing genotypes

Issue - State: closed - Opened by traxexx about 5 years ago

#34 - GT-825 v2.4a release

Pull Request - State: closed - Opened by traxexx about 5 years ago

#33 - Latest docker image not working

Issue - State: closed - Opened by vandhanak about 5 years ago - 3 comments

#32 - idxdepth underestimating depth of coverage, possibly?

Issue - State: closed - Opened by dantaki over 5 years ago - 2 comments

#31 - multigrmpy.py: Illegal header name "depth sd"

Issue - State: closed - Opened by dantaki over 5 years ago - 3 comments

#30 - GT-808 v2.3 release

Pull Request - State: closed - Opened by traxexx over 5 years ago

#29 - Runtime exceeds expectations

Issue - State: closed - Opened by WEClarke over 5 years ago - 2 comments

#28 - Genotype does not meet VCF 4.2 spec

Issue - State: closed - Opened by WEClarke over 5 years ago - 3 comments

#27 - idxdepth error

Issue - State: closed - Opened by RSherman15 over 5 years ago - 10 comments

#26 - Manifest ID column name should be lowercase "id"

Issue - State: closed - Opened by traxexx over 5 years ago

#25 - GT-804 v2.2b release

Pull Request - State: closed - Opened by traxexx over 5 years ago

#24 - required version of python

Issue - State: closed - Opened by KamilSJaron over 5 years ago - 5 comments

#23 - Native build seems to point to wrong boost library

Issue - State: closed - Opened by RSherman15 over 5 years ago - 4 comments

#22 - GT-802 update license and docker

Pull Request - State: closed - Opened by traxexx over 5 years ago

#21 - Alternate reference based on paragraph results

Issue - State: closed - Opened by wyim-pgl over 5 years ago - 2 comments

#20 - comparison to svtyper

Issue - State: closed - Opened by brentp over 5 years ago - 10 comments

#19 - make dockerfile work

Pull Request - State: closed - Opened by brentp over 5 years ago - 2 comments

#18 - build commands are out-dated

Issue - State: closed - Opened by brentp over 5 years ago - 4 comments

#17 - how to run on large cohort

Issue - State: closed - Opened by brentp over 5 years ago - 3 comments

#16 - GT-743 v2.2 release

Pull Request - State: closed - Opened by traxexx over 5 years ago

#15 - Dockerfile entry point does not match documentation

Issue - State: closed - Opened by WEClarke over 5 years ago - 2 comments

#14 - Unable to compile without errors

Issue - State: closed - Opened by MaestSi almost 6 years ago - 6 comments

#13 - GT-683 v2.1 release

Pull Request - State: closed - Opened by traxexx almost 6 years ago - 1 comment

#12 - Reference sequences do not match error messages would be helpful

Issue - State: closed - Opened by RSherman15 almost 6 years ago - 1 comment

#11 - Fix docker build

Pull Request - State: closed - Opened by pkrusche about 6 years ago - 1 comment

#10 - More fixes for included Boost build

Pull Request - State: closed - Opened by pkrusche over 6 years ago

#9 - Include a copy / subset of Boost in-source

Pull Request - State: closed - Opened by pkrusche over 6 years ago - 1 comment

#8 - GH4: Fix graph-tools build warning

Pull Request - State: closed - Opened by felixschlesinger over 6 years ago - 1 comment

#7 - Travis CI support

Pull Request - State: closed - Opened by pkrusche over 6 years ago - 2 comments

GitHub / illumina/paragraph issues and pull requests