fulcrumgenomics/fgbio issues and pull requests

#908 - Exact UMI from read name

Issue - State: open - Opened by xianantwist almost 2 years ago - 2 comments
Labels: question

#907 - Add option to maintain N in umi

Pull Request - State: open - Opened by JoeVieira almost 2 years ago - 6 comments
Labels: needs review

#906 - Use GroupReadsByUmi for standard duplicate marking?

Issue - State: open - Opened by eboyden almost 2 years ago - 8 comments
Labels: enhancement, help wanted

#905 - GroupReadsByUmi "identity" may be unnecessary?

Issue - State: open - Opened by eboyden almost 2 years ago
Labels: enhancement, help wanted

#904 - GroupReadsByUmi Error - multiple non-secondary, non-supplemental R1s

Issue - State: closed - Opened by saradunaj almost 2 years ago - 8 comments
Labels: question

#903 - Does CallDuplexConsensusReads require overlapping read pairs?

Issue - State: closed - Opened by mulderdt almost 2 years ago - 2 comments
Labels: question

#902 - ZipperBams error about RGID

Issue - State: open - Opened by esamorodnitsky almost 2 years ago - 6 comments
Labels: enhancement, help wanted, question

#901 - BWA mem -Y did not make a difference in consensus calling

Issue - State: closed - Opened by esamorodnitsky almost 2 years ago - 1 comment
Labels: question

#900 - CallMolecularConsensusReads with multiple threads causing a core dump

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

#899 - CallMolecularConsensusReads vs. CallOverlappingConsensusBases vs. CallDuplexConsensusReads

Issue - State: open - Opened by esamorodnitsky almost 2 years ago - 4 comments

#898 - How exactly does CallMolecularConsensusReads work?

Issue - State: closed - Opened by noranekonobokkusu about 2 years ago - 4 comments
Labels: question

#897 - Improve docs for consensus reads being unaligned

Pull Request - State: closed - Opened by nh13 about 2 years ago - 1 comment

#896 - Is CallDuplexConsensusReads supposed to outputs reads as unmapped bam?

Issue - State: closed - Opened by karlbeutner about 2 years ago - 5 comments
Labels: question

#895 - How does CallDuplexConsensusReads handle homopolymers?

Issue - State: closed - Opened by karlbeutner about 2 years ago - 2 comments
Labels: question

#894 - Update ZipperBams to state the sort is checked in the SAM header

Pull Request - State: closed - Opened by nh13 about 2 years ago - 1 comment

#893 - Tool to downsample a BAM while retaining reads in low coverage areas.

Pull Request - State: closed - Opened by tfenne about 2 years ago - 1 comment

#892 - Specific reads used for each consensus sequence

Issue - State: closed - Opened by karlbeutner about 2 years ago - 2 comments
Labels: question

#891 - Yf coverage unifier

Pull Request - State: open - Opened by yfarjoun about 2 years ago

#890 - Write a guide on "so you have UMIs in your data, here's how to get to a standardized BAM" with fgbio

Issue - State: open - Opened by nh13 about 2 years ago

#889 - require-single-strand-agreement on BAM that contains both duplex and single-strand consensus reads

Issue - State: open - Opened by gevro about 2 years ago - 1 comment

#888 - Zipperbams error:

Issue - State: closed - Opened by gevro about 2 years ago - 10 comments

#887 - Filterconsensusreads before vs after mapping

Issue - State: open - Opened by gevro about 2 years ago - 1 comment

#886 - CallOverlappingConsensusBases vs "consensus-call-overlapping-bases" in CallDuplexConsensusReads

Issue - State: open - Opened by gevro about 2 years ago - 1 comment

#885 - Error:Could not find dictionary next to reference file

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

#884 - Bump htsjdk to 3.0.3

Pull Request - State: closed - Opened by clintval about 2 years ago - 4 comments

#883 - SetMateInformation failed

Issue - State: open - Opened by SR5590 about 2 years ago - 1 comment
Labels: question

#882 - CallDuplexConsensusReads Raw Reads Filtered Due to Not Enough Reads

Issue - State: open - Opened by ARE4S about 2 years ago - 8 comments
Labels: bug

#881 - Tweak the size of caches for parallel consensus calling down to reduc…

Pull Request - State: closed - Opened by tfenne about 2 years ago - 4 comments

#880 - SetMateInformation: Input is not queryname sorted or grouped

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

#879 - AnnotateBamWithUmis, sorted or unsorted BAMs? code example?

Issue - State: open - Opened by sofiapuvogelvittini over 2 years ago - 3 comments
Labels: question

#878 - feature request: switch order of operations for ClipBam

Issue - State: open - Opened by eboyden over 2 years ago - 4 comments
Labels: enhancement, help wanted

#877 - question: need to correct MD/NM/UQ tags multiple times on piped commands or not?

Issue - State: open - Opened by eboyden over 2 years ago - 4 comments

#876 - feature request: combine AssignPrimers and TrimPrimers into a single tool

Issue - State: open - Opened by eboyden over 2 years ago - 7 comments
Labels: question

#875 - CorrectUmis metrics file: extra line with Ns

Issue - State: closed - Opened by gshiba over 2 years ago - 2 comments
Labels: question

#874 - CallMolecularConsensusReads `--min-reads `

Issue - State: closed - Opened by migrau over 2 years ago - 3 comments
Labels: question

#873 - Add UMIs to fastq

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

#872 - anyway to indentify the consensus reads with umi group size = 1 in the consensus fastq gz file (set min group size == 1) in umi process

Issue - State: closed - Opened by linuxbioinfoguy over 2 years ago - 1 comment
Labels: question

#871 - Add an option to skip the mate cigar in EstimateRnaSeqInsertSize

Pull Request - State: open - Opened by nh13 over 2 years ago - 1 comment
Labels: needs review

#870 - CallMolecularConsensusReads failing

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

#869 - 5’-3’ origin of UMIs

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

#868 - [feat] Add an option to sort by sequence role in CollectAlternateContigNames

Pull Request - State: open - Opened by nh13 over 2 years ago - 1 comment
Labels: needs review

#867 - Expose chunkSize parameter in CallDuplexConsensusReads

Pull Request - State: open - Opened by mjhipp over 2 years ago - 3 comments

#866 - Best practices CallDuplexConsensusReads with min-reads= 1 1 0

Issue - State: closed - Opened by tobyaicher over 2 years ago - 1 comment
Labels: question

#865 - A different patch for issue 858

Pull Request - State: closed - Opened by tfenne over 2 years ago

#864 - [bugfix] fix issue #858 in CallDuplexConsensusReads

Pull Request - State: closed - Opened by nh13 over 2 years ago - 1 comment

#863 - Best practices ZipperBam after CallDuplexConsensusReads

Issue - State: closed - Opened by tobyaicher over 2 years ago - 1 comment
Labels: question

#862 - Unexpected Consensus Sequence When Using CallMolecularConsensusReads

Issue - State: closed - Opened by bebelya over 2 years ago - 6 comments
Labels: question

#861 - Error in CallMolecularConsensusReads

Issue - State: closed - Opened by bebelya over 2 years ago - 4 comments
Labels: question

#860 - bugfix: ReviewConsensusVariants should not require grouped raw reads to

Pull Request - State: closed - Opened by nh13 over 2 years ago - 2 comments

#859 - Fix a bug where consensus reads are produced with zero depth

Pull Request - State: closed - Opened by nh13 over 2 years ago - 1 comment

#858 - Error in FilterConsensusReads

Issue - State: closed - Opened by dstephensSD over 2 years ago - 5 comments
Labels: bug

#857 - GroupReadsByUMI produces snappy error

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

#856 - Error: Sample at ordinal #1 is missing: Sample_ID

Issue - State: closed - Opened by Phylloxera over 2 years ago - 6 comments
Labels: question

#855 - "Too many open files" when running DemuxFastqs on large sequencing run

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

#854 - Added ncRNA biotype to NCBI RefSeq GFF parser.

Pull Request - State: closed - Opened by tfenne over 2 years ago

#853 - Multiple non-secondary, non-supplemental R1s Error

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

#852 - ExtractUmisFromBam "Read was not the second end of a pair" Error

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

#851 - bug in CallMolecularConsensusRead?

Issue - State: closed - Opened by ruolin over 2 years ago - 6 comments
Labels: question

#850 - Fix overly aggressive overlap-clipping regressions in ClipBam

Pull Request - State: closed - Opened by jrm5100 over 2 years ago - 2 comments

#849 - Regression in `ClipBam` in Fgbio v2.

Issue - State: closed - Opened by jrm5100 over 2 years ago

#848 - Adding a code of conduct

Pull Request - State: closed - Opened by nh13 over 2 years ago - 1 comment

#847 - FilterConsensusReads --min-reads=1 1 0 requirement failed: Expected the AB-strand to have depth > 0 for read: BJ22CM006291R:2660272 1/2 1b unmapped read

Issue - State: open - Opened by angeladarling over 2 years ago - 5 comments

#846 - Update codecov version

Pull Request - State: closed - Opened by nh13 over 2 years ago - 1 comment

#845 - Add a missing param to constructor of StreamingPileupBuilder via apply

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

#844 - ZipperBams vs bwa mem -C

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

#843 - Calling both duplex and single-strand consensus sequences

Issue - State: closed - Opened by tobyaicher over 2 years ago - 4 comments
Labels: question

#842 - [bugfix] SamRecordClipper.clipOverlappingReads now accounts for soft-clipped bases starting before the ends

Pull Request - State: closed - Opened by jrm5100 over 2 years ago - 3 comments
Labels: bug

#841 - FilterConsensusReads error

Issue - State: closed - Opened by fengdong110 over 2 years ago - 1 comment

#840 - Check that alleles in calls are a subset of the variant alleles in VcfBuilder

Issue - State: open - Opened by nh13 over 2 years ago
Labels: enhancement

#839 - Should fastqs be trimmed after ExtractUmisFromBam and before GroupReadsByUmi?

Issue - State: closed - Opened by xiucz over 2 years ago - 3 comments
Labels: question

#838 - Update scala-xml to a much more recent version

Pull Request - State: closed - Opened by tfenne over 2 years ago

#837 - Check for UMI swapping

Issue - State: open - Opened by blackbeerd over 2 years ago - 7 comments
Labels: enhancement

#836 - Remove VariantContexts from most fgbio tools

Pull Request - State: open - Opened by kstromhaug over 2 years ago - 1 comment

#835 - My fgbio pipeline worked for 1.5.1 but not 2.0.0. Why?

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

#834 - `CigarStats.apply` could give better error if internal clipping operators found

Issue - State: open - Opened by mjhipp over 2 years ago
Labels: enhancement

#833 - FilterConsensusReads --min-reads 1 0 0 vs --min-reads 0 0 0; Why do they differ?

Issue - State: open - Opened by dstephensSD over 2 years ago - 4 comments
Labels: question

#832 - Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests

Pull Request - State: open - Opened by kstromhaug over 2 years ago - 1 comment

#831 - CallDuplexConsensusReads hard-clips ONE of the two duplex reads

Issue - State: open - Opened by genegolts over 2 years ago - 14 comments
Labels: question

#830 - The minimum number of reads supporting a consensus base/read.

Issue - State: open - Opened by asmlgkj over 2 years ago - 6 comments
Labels: question

#829 - Ensure SamWriter always logs how many it wrote before close()

Pull Request - State: closed - Opened by clintval over 2 years ago - 3 comments

#828 - Should consensus calling trim back to the _unclipped end_ versus the aligned end of its mate

Issue - State: open - Opened by nh13 over 2 years ago
Labels: question

#827 - Does DemuxFastqs mismatch option apply to each barcode individually?

Issue - State: closed - Opened by denriquez almost 3 years ago - 3 comments
Labels: question

#826 - Add metric builder and sorter

Pull Request - State: open - Opened by nh13 almost 3 years ago - 2 comments

#825 - [bugfix] metrics are now updated and logged in the overlapping bases

Pull Request - State: closed - Opened by nh13 almost 3 years ago - 1 comment

#824 - [bugfix] overlapping consensus caller should examine only

Pull Request - State: closed - Opened by nh13 almost 3 years ago - 1 comment
Labels: bug

#821 - Where to insert Picard MarkIlluminaAdapters in an fgbio workflow?

Issue - State: closed - Opened by blackbeerd almost 3 years ago - 21 comments
Labels: question

#812 - `VcfWriter` does not write VCF index files anymore

Issue - State: closed - Opened by mjhipp almost 3 years ago - 2 comments
Labels: bug

#796 - Turn off codacy

Issue - State: closed - Opened by nh13 almost 3 years ago - 1 comment

#760 - Add an entrypoint to SamSource for bytes of SAM/BAM/CRAM

Pull Request - State: open - Opened by clintval about 3 years ago - 2 comments

#744 - SamToFastq ERROR

Issue - State: open - Opened by zhangyafeng1 about 3 years ago - 9 comments
Labels: bug

#739 - Command line tool to produce and print pairwise alignments.

Pull Request - State: open - Opened by tfenne about 3 years ago - 2 comments

#677 - Add End Repair Artifact Filter to FilterSomaticVcf

Pull Request - State: closed - Opened by ThomasHSmith over 3 years ago - 3 comments

#604 - NoSuchElementException with ReviewConsensusVariants

Issue - State: closed - Opened by agagarega over 4 years ago - 13 comments
Labels: question

#570 - GroupReadsByUmi [Paired strategy used but umi did not contain 2 segments]

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

#557 - CorrectUmis: allow for different length UMIs

Issue - State: open - Opened by fgvieira about 5 years ago - 12 comments
Labels: help wanted, question

#556 - CallDuplexConsensusReads Raw Reads Filtered Due to Not Enough Reads

Issue - State: closed - Opened by doranlab about 5 years ago - 6 comments
Labels: question

#553 - Store UMI base quals as SAM tag(s) with ExtractUmisFromBam

Pull Request - State: closed - Opened by 09aaronl about 5 years ago - 2 comments
Labels: enhancement

#508 - Add tooling & docs to replace picard's SamToFastq and MergeBamAlignment

Issue - State: closed - Opened by tfenne over 5 years ago - 3 comments
Labels: enhancement, help wanted

#433 - CollectDuplexSeqMetrics error

Issue - State: closed - Opened by xujishu over 6 years ago - 7 comments
Labels: question

#391 - fgbio for Agilent

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

GitHub / fulcrumgenomics/fgbio issues and pull requests