Illumina paragraph issues

Illumina / paragraph

Graph realignment tools for structural variants

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issues

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Whole Exome Data?

#85 bbimber opened 3 months ago
0
BAM header only has a subset of the reference chromosomes -- please make sure they match!

#84 pingxinxing opened 4 months ago
0
Distance between vcf position and chrom start is smaller than read length.

#83 pingxinxing opened 4 months ago
0
[BUG] Error adding alt from insertion sequence representing a duplication

#82 rickymagner opened 7 months ago
0
Format error in vcf line:

#81 mrwangyz opened 1 year ago
3
Issue's with Native Build and Boost

#80 david2905 opened 1 year ago
0
Add support for VCFv4.2 breakend notation

#79 nvnieuwk opened 1 year ago
0
Error when working with `--ins-info-key`

#78 nvnieuwk opened 1 year ago
1
Problem starting the script multigrmpy.py

#77 aaaniich opened 1 year ago
2
idxdepth regex option not working

#76 weilu1998 closed 1 year ago
0
Genotyping for SNP

#75 Wangchangsh opened 1 year ago
0
Stop using Werror and Wall

#74 dpryan79 opened 1 year ago
0
Install paragraph

#73 vanhoan310 opened 2 years ago
0
no BGZF EOF marker

#72 xuefenfei712 opened 2 years ago
0
How to merge multi-samples SVs and obtain breakpoints for genotyping a population

#71 Zhiliang-Zhang opened 2 years ago
0
Added tabix indexing of variants.vcf.gz file

#70 ivargr opened 2 years ago
0
index file

#69 MehmetGoktay opened 2 years ago
0
grmpy error: [E::cram_itr_query]

#68 jasonbhn opened 3 years ago
0
subprocess.CalledProcessError

#67 duzezhen closed 3 years ago
2
--vcf-split option with no description

#66 shangshanzhizhe opened 3 years ago
0
Missing key SEQ for <INS>

#65 brentp opened 3 years ago
6
Error with idxdepth: "Assertion failed: _impl->header_contig_map.count(chr) != 0"

#64 cassisnaro opened 3 years ago
1
ValueError: Invalid VariantRecord. Number of samples does not match header

#63 YPGG1234 closed 3 years ago
2
Can paragraph be used for indel from 2 bp to 30 bp?

#62 349539427 opened 3 years ago
1
Exception: Different padding base for REF and ALT

#61 srbehera opened 3 years ago
6
Errors on idxdepth

#60 Yexin-Zhang opened 3 years ago
4
[E::idx_find_and_load] Could not retrieve index file

#59 Xuelei-Dai opened 3 years ago
7
How to reuse variants converted from vcf to json for population genotyping?

#58 malemay opened 3 years ago
0
Pysam error message after paragraph genotyping completes

#57 mchowdh200 closed 3 years ago
2
Which aligner?

#56 fergsc closed 3 years ago
2
Trouble genotyping lifted variants

#55 Parsoa closed 3 years ago
2
Handling of temporary files by multigrmpy.py

#54 malemay closed 3 years ago
2
Genotyping unresolved insertions using reads around the breakpoint

#53 malmarri closed 3 years ago
1
How to better call and genotype population SVs?

#52 biozzq closed 3 years ago
4
Compatibility of paragraph and Sniffles VCF

#51 biozzq closed 3 years ago
4
SV calling and genotyping across a population

#50 biozzq closed 4 years ago
2
idxdepth error

#49 biozzq closed 3 years ago
3
Errors when make

#48 heyaoxi closed 4 years ago
2
Using more than one input VCF file

#47 martinghunt closed 3 years ago
1
error reference_sequence.empty

#46 KamilSJaron closed 3 years ago
9
Missing key {ins_info_key} for <INS> at {self.chrom}:{vcf.pos};

#45 Parsoa closed 4 years ago
1
Stripping END tag in INFO field

#44 WEClarke closed 4 years ago
3
Error processing an INV

#43 jjfarrell closed 3 years ago
6
Compatibility of paragraph and manta

#42 KamilSJaron closed 4 years ago
13
How to prepare vcf file for Duplication & Tandem Duplication?

#41 Zhiliang-Zhang closed 4 years ago
3
Pysam error

#40 jjfarrell closed 3 years ago
6
INS error

#39 asylvz closed 4 years ago
6
Distance between vcf position and chrom start is smaller than read length.

#38 MaoYafei closed 4 years ago
3
Illegal character in reference sequence (W base and possibly other noncanonical bases)

#37 dantaki closed 5 years ago
2
Complex structural variants like TRA or INVDUP

#36 quanc1989 closed 5 years ago
2