ExaScience/elprep issues and pull requests

#74 - invalid BGZF file: does not end in proper EOF marker

Issue - State: open - Opened by lucy-1n-the-ai 3 months ago - 1 comment

#73 - elprpe vcf-to-elsites dbSNP_156.vcf dbSNP_156.elsites [Killed]

Issue - State: open - Opened by QifengSun about 1 year ago

#72 - Use ASCIISet

Pull Request - State: open - Opened by elliotwutingfeng over 1 year ago

#71 - NO_COOR error when trying to index the output bam file

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

#70 - build fails on ALMA linux 9

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

#69 - Option to output realigned BAM file during --haplotypecaller step

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

#68 - elfasta-conversion error: bufio.Scanner: token too long

Issue - State: open - Opened by desmodus1984 over 1 year ago - 6 comments

#67 - Very low number of variants called by elprep in an heterozygous genome

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

#66 - feature: index output

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

#65 - elprep merge: add input for intermediate files

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

#64 - header tag differs between runs

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

#63 - Add wiki page about "creating your own `sfm` script"

Issue - State: open - Opened by matthdsm over 2 years ago - 3 comments

#62 - `elprep split` output directory

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

#61 - elprep5: gVCF does not match BAM read pileup

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

#60 - coverage vs vcf.gz size discrepancy

Issue - State: closed - Opened by desmodus1984 over 2 years ago - 4 comments

#59 - Proper running using sam input file?

Issue - State: open - Opened by desmodus1984 almost 3 years ago - 1 comment

#58 - vcf-to-elsites

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

#57 - "exit status 2" error

Issue - State: open - Opened by yanlolo almost 3 years ago - 2 comments

#56 - Variant calling using `sfm` does not adhere to thread limit

Issue - State: open - Opened by matthdsm about 3 years ago - 13 comments

#55 - Issue during build of v5.1.0

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

#54 - GATK equivalency - version

Issue - State: closed - Opened by matthdsm about 3 years ago - 1 comment

#53 - Comment: handling RG's in SFM

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

#52 - [RFE] haplotypecaller: support for custom GVCF GQ slices

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

#51 - sfm --haplotypecaller introduces duplicate lines in BAM

Issue - State: open - Opened by ntm over 3 years ago - 2 comments

#50 - exit status 2

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

#49 - Doing just variant calling /haplotypecaller? non-model organism no known-variant file for bqsr

Issue - State: open - Opened by desmodus1984 over 3 years ago - 7 comments

#48 - Add conda install suggestion, add badges

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

#47 - Support for multiple input files

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

#46 - BQSR filters out reads 'not in target region'

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

#45 - Converting a dbsnp vcf to elsites uses a lot of resources

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

#44 - Estimate RAM usage based on input filesize

Issue - State: open - Opened by matthdsm over 3 years ago - 14 comments

#43 - How to call population snps/indels?

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

#42 - Is this a reasonable way to limit default threads used

Issue - State: closed - Opened by jbh-cas over 3 years ago - 3 comments

#41 - More memory needed than samtools on 1CPU

Issue - State: closed - Opened by Juke34 over 3 years ago - 3 comments

#40 - panic: interface conversion: interface {} is nil, not string

Issue - State: closed - Opened by Juke34 almost 4 years ago - 2 comments

#39 - Update README.md

Pull Request - State: closed - Opened by Juke34 almost 4 years ago - 2 comments

#38 - UMI's and duplicate marking

Issue - State: open - Opened by matthdsm about 4 years ago - 1 comment

#37 - elprep sfm run failed due to insufficient RAM

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

#36 - Secondary .bai files

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

#35 - Unclipped position not present in SAM alignment

Issue - State: closed - Opened by babicjovana about 4 years ago - 9 comments

#34 - Does the command remove duplicates also does the marking of the duplicates?

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

#33 - Encapsulate format conversions into elprep

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

#32 - filter mismatches and or percentage identity?

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

#31 - How to control compression level of output?

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

#30 - elprep sfm mode exits with out of Memory error

Issue - State: closed - Opened by ajayrv over 4 years ago - 9 comments

#29 - Feature request: working with limits on VMEM

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

#28 - Large amount of diskspace required

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

#27 - Q: support for PacBio "native" format

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

#26 - MapReduce markdup

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

#25 - Compilation problems

Issue - State: closed - Opened by bvalot over 5 years ago - 1 comment

#24 - Fix parsing bam files containing float

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

#23 - BaseRecalibrator maxCycle

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

#22 - Warning: The --sqq optional flag is set without using --bqsr.

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

#21 - Question about the paper

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

#20 - testing?

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

#19 - panic: runtime error: index out of range

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

#18 - sfm sorting problem

Issue - State: closed - Opened by geertvandeweyer almost 6 years ago - 7 comments

#17 - Added option to set tmpPath for sfm

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

#16 - corrected typos

Pull Request - State: closed - Opened by colindaven about 6 years ago - 2 comments

#15 - python script handing of `single-end` flag

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

#14 - Feature discussion: avoiding samtools calls

Issue - State: closed - Opened by matthdsm over 6 years ago - 5 comments

#13 - added MAPQ filter

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

#12 - Feature request: Add quality filter

Issue - State: closed - Opened by matthdsm over 6 years ago

#11 - Bioconda recipe

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

#10 - clean main func

Pull Request - State: closed - Opened by dvrkps almost 7 years ago - 1 comment

#9 - Optional tags filter

Pull Request - State: closed - Opened by caherzee about 7 years ago

#8 - Added a filter to output perfectly mapping reads only (soft-clipping ok)

Pull Request - State: closed - Opened by leonorpalmeira about 7 years ago

#7 - error while trying to split

Issue - State: closed - Opened by RichardCorbett over 9 years ago - 29 comments

GitHub / ExaScience/elprep issues and pull requests