bioinform/somaticseq issues and pull requests

#135 - some indels had frequency of zero.

Issue - State: open - Opened by zenghp365 2 months ago - 2 comments

#134 - makeSomaticScripts.py "single" generated command incorrectly passes vcf.gz file to option -d of lofreq call.

Issue - State: closed - Opened by harrymatthews50 3 months ago - 2 comments

#133 - snakemake implementation support tumour-only samples.

Issue - State: open - Opened by harrymatthews50 3 months ago - 1 comment

#132 - ntree_limit deprecated into iteration_range in xgboost>=1.4

Pull Request - State: closed - Opened by litaifang 8 months ago

#131 - AI consensus calling error on WGS samples

Issue - State: open - Opened by GACGAMA 8 months ago - 7 comments

#130 - Error when running FFPE training data from SEQ2C

Issue - State: closed - Opened by GACGAMA 8 months ago - 5 comments

#129 - Are multi-nucleotide and complex variants ignored?

Issue - State: open - Opened by rebber 9 months ago - 2 comments

#128 - how to obtain all variants where the "FILTER" column is not labeled as "PASS"

Issue - State: closed - Opened by xiechangxiao 10 months ago - 1 comment

#127 - UnboundLocalError: cannot access local variable 'normal_name' where it is not associated with a value

Issue - State: closed - Opened by SAADAT-Abu about 1 year ago - 10 comments

#126 - Output allele of the normal sample

Issue - State: open - Opened by fredsamhaak about 1 year ago - 2 comments

#125 - Error when running makeSomaticScripts with multiple threads

Issue - State: closed - Opened by GACGAMA about 1 year ago - 3 comments

#124 - Dockerized alignment workflow does not work with multiple input files

Issue - State: closed - Opened by GACGAMA over 1 year ago - 5 comments

#123 - Applying internal filters to outputs before running SomaticSeq

Issue - State: closed - Opened by ronkesm over 1 year ago - 1 comment

#122 - somaticseq failing for same command it had previously successfully run

Issue - State: closed - Opened by csreej27 over 1 year ago - 11 comments

#121 - Ground Truths required for training

Issue - State: closed - Opened by harish0201 over 1 year ago - 1 comment

#120 - Where are the 10x Genomics single-cell copy number variation (CNV) analysis results?

Issue - State: closed - Opened by genetronhealth over 1 year ago - 7 comments

#119 - Question for the paper on establishing the reference call set

Issue - State: closed - Opened by FriederikeHanssen over 1 year ago - 3 comments

#118 - Slow RNA variant calling

Issue - State: open - Opened by katjur01 over 1 year ago - 8 comments

#117 - Somaticseq makeSomaticScripts.py running and output issues

Issue - State: closed - Opened by csreej27 almost 2 years ago - 8 comments

#116 - SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed

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

#115 - Docker issue with latest version

Issue - State: closed - Opened by emucaki about 2 years ago - 1 comment

#114 - Pretrained Classifier

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

#113 - Question about simulating somatic mutations

Issue - State: closed - Opened by leedchou over 2 years ago - 7 comments

#112 - Special setting for b37?

Issue - State: closed - Opened by yoda0612 over 2 years ago - 14 comments

#111 - Result of TNscope caller

Issue - State: closed - Opened by yoda0612 over 2 years ago - 4 comments

#110 - Filter truth vcf files for dbsnp?

Issue - State: closed - Opened by iserf over 2 years ago - 1 comment

#109 - somatic_xgboost.py train: xgboost.core.XGBoostError

Issue - State: closed - Opened by iserf over 2 years ago

#108 - SV truthset for SEQC

Issue - State: closed - Opened by miyakokodama over 2 years ago - 1 comment

#107 - makeSomaticScripts.py single mode passing certain arguments

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

#106 - generating training data using single medium-coverage replicate of normal sample

Issue - State: closed - Opened by kiranchari over 2 years ago - 1 comment

#105 - must the mutation spike-in singularity pipeline be processed in a single HPC run?

Issue - State: closed - Opened by kiranchari almost 3 years ago - 2 comments

#104 - AssertionError in makeSomaticScripts.py

Issue - State: closed - Opened by Fer020707 almost 3 years ago - 8 comments

#103 - UnboundLocalError: local variable 'normal_name' referenced before assignment

Issue - State: closed - Opened by zhangbiwu almost 3 years ago - 14 comments

#102 - Recommendations for using your thoroughly vetted High Confidence regions.

Issue - State: closed - Opened by SSunkara almost 3 years ago - 2 comments

#101 - Question: How is the final VAF of variant calculated?

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

#100 - Error: Training with Strelka leads to Error

Issue - State: closed - Opened by robinjugas over 3 years ago - 11 comments

#99 - SomaticSeq Prediction Error

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

#98 - stat /opt/somaticseq/utilities/split_mergedBed.py: no such file or directory error

Issue - State: closed - Opened by jeongmeani almost 4 years ago - 3 comments

#97 - Prediction output files interpretations

Issue - State: closed - Opened by wjianga almost 4 years ago - 3 comments

#96 - Question about SEQ-II datasets

Issue - State: closed - Opened by LeiHaoa almost 4 years ago - 4 comments

#95 - In training mode, error: invalid choice.

Issue - State: closed - Opened by wjianga almost 4 years ago - 4 comments

#94 - Output files when running Consensus mode

Issue - State: closed - Opened by wjianga almost 4 years ago - 2 comments

#93 - omitted some columns of tsv in somatic_vcf2tsv.py

Issue - State: closed - Opened by jeongmeani almost 4 years ago - 11 comments

#92 - bamSimulator result shows a lot of false positives

Issue - State: closed - Opened by LeiHaoa almost 4 years ago - 4 comments

#91 - model overfitting

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

#90 - failed prediciton

Issue - State: closed - Opened by gianfilippo about 4 years ago - 3 comments

#89 - clarification: ada_model_builder_ntChange.R vs ada_model_builder.R

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

#88 - Ensemble.sSNV.tsv does not have some vardict variant.

Issue - State: closed - Opened by jeongmeani about 4 years ago - 8 comments

#87 - multi-thread run clarification

Issue - State: closed - Opened by gianfilippo about 4 years ago - 23 comments

#86 - submit_callers_multiThreads.sh missing "split" in call to submit_JointSNVMix2.sh

Issue - State: closed - Opened by gianfilippo about 4 years ago - 7 comments

#85 - singularity submit_SomaticSeq.sh code error ?

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

#84 - dockered VarScan2 issue

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

#83 - dockered vardict issue

Issue - State: closed - Opened by gianfilippo over 4 years ago - 11 comments

#82 - docker error - docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "process_linux.go:319: getting the final child's pid from pipe caused \"EOF\"": unknown.

Issue - State: closed - Opened by jeongmeani over 4 years ago - 8 comments

#81 - Error: In training mode, there must be both true positives and false positives in the call set

Issue - State: closed - Opened by vymao over 4 years ago - 21 comments

#80 - Ranksums

Pull Request - State: closed - Opened by litaifang over 4 years ago

#79 - Some clarifications?

Issue - State: closed - Opened by vymao over 4 years ago - 8 comments

#78 - Error: In training mode, there must be both true positives and false positives in the call set.

Issue - State: closed - Opened by gianfilippo over 4 years ago - 8 comments

#77 - RealignerTargetCreator and IndelRealigner steps

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

#76 - No succesful mutations?

Issue - State: closed - Opened by adfnih almost 5 years ago - 2 comments

#75 - slurm vs sge

Issue - State: closed - Opened by cbiitbian almost 5 years ago - 12 comments

#74 - Strelka parameters on targeted amplicon panels, single mode (only tumor sample). Using the docker file for run.

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

#73 - addsnv.py ERROR/WARNINGS: encountered error in mutation spikein; could not pileup for region

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

#72 - ImportError: libcurl.so.4: cannot open shared object file: No such file or directory

Issue - State: closed - Opened by gianfilippo almost 5 years ago - 7 comments

#71 - request for examples

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

#70 - somatic mutation spike in pipeline without docker

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

#69 - freebayes or other callers

Issue - State: closed - Opened by gianfilippo almost 5 years ago - 4 comments

#68 - Error with somaticseq_parallel.py

Issue - State: closed - Opened by joonlee3 over 5 years ago - 3 comments

#67 - default processing run_somaticseq.py

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

#66 - Exception: LoFreq.snvs.concat.vcf.gz does not seem to be properly sorted

Issue - State: closed - Opened by t-neumann almost 6 years ago - 2 comments

#65 - GATK4 Mutect2

Issue - State: closed - Opened by fpbarthel about 6 years ago - 2 comments

#64 - update somaticseq on anaconda

Issue - State: closed - Opened by fpbarthel about 6 years ago - 10 comments

#63 - Using somaticseq for somatic calls in non-human species and tumor-only mode

Issue - State: closed - Opened by sbamin about 6 years ago - 4 comments

#62 - Fastq2bam

Issue - State: closed - Opened by esherafat about 6 years ago - 2 comments

#61 - Please release a version

Issue - State: closed - Opened by rhpvorderman about 6 years ago - 2 comments

#60 - V3.nightly

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

#59 - V3.nightly

Pull Request - State: closed - Opened by litaifang about 6 years ago

#58 - Arguments for each caller

Issue - State: closed - Opened by Tato14 over 6 years ago - 1 comment

#57 - SomaticSeq for targeted panel data

Issue - State: closed - Opened by Tato14 over 6 years ago - 11 comments

#56 - Normalized multiallelic indels in CombineVariants_MVJSD.indel.vcf excluded from Ensemble.tsv

Issue - State: closed - Opened by pkothiyal over 6 years ago - 3 comments

#55 - Merge Li-Tai's new change to LY branch

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

#54 - 2.7.1

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

#53 - 2.7.1

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

#52 - SomaticSeq.Wrapper.sh should support GATK4

Issue - State: closed - Opened by 0xaf1f over 6 years ago - 1 comment

#51 - Improve documentation for snakemake workflow and link from top-level README

Pull Request - State: closed - Opened by 0xaf1f over 6 years ago - 1 comment

#50 - Snakemake corrections

Pull Request - State: closed - Opened by 0xaf1f over 6 years ago - 7 comments

#49 - Add a Snakemake-based workflow

Pull Request - State: closed - Opened by 0xaf1f almost 7 years ago - 4 comments

#48 - Could you provide documentation on the 70 features extracted by somaticseq? Trying to better understand SomaticSeq's model

Issue - State: closed - Opened by kiranchari almost 7 years ago - 2 comments

#47 - V2.7.0

Pull Request - State: closed - Opened by litaifang almost 7 years ago

#46 - No sample information error

Issue - State: closed - Opened by mingyi-wang almost 7 years ago - 12 comments

#45 - submitSomaticSniper: unable to open file /mnt/<path-to-RESULTS>/1/1.bed

Issue - State: closed - Opened by 0xaf1f almost 7 years ago - 7 comments

#44 - V2.6.0

Pull Request - State: closed - Opened by litaifang almost 7 years ago

#43 - hg19 and b37

Issue - State: closed - Opened by mingyi-wang almost 7 years ago - 1 comment