Issues

• HaplotypeCaller on single-end data

  ExaScience/elprep#75 · Filter by author SimonaSecomandi opened on Feb 4, 2025
  3

• invalid BGZF file: does not end in proper EOF marker

  ExaScience/elprep#74 · Filter by author lucy-1n-the-ai opened on Jul 27, 2024
  1

• elprpe vcf-to-elsites dbSNP_156.vcf dbSNP_156.elsites [Killed]

  ExaScience/elprep#73 · Filter by author QifengSun opened on Oct 18, 2023

• NO_COOR error when trying to index the output bam file

  ExaScience/elprep#71 · Filter by author ghost opened on Apr 4, 2023

• build fails on ALMA linux 9

  ExaScience/elprep#70 · Filter by author ntm opened on Mar 21, 2023

• Option to output realigned BAM file during --haplotypecaller step

  ExaScience/elprep#69 · Filter by author leonorpalmeira opened on Mar 16, 2023

• elfasta-conversion error: bufio.Scanner: token too long

  ExaScience/elprep#68 · Filter by author desmodus1984 opened on Feb 28, 2023
  6

• Very low number of variants called by elprep in an heterozygous genome

  ExaScience/elprep#67 · Filter by author chklopp opened on Feb 14, 2023

• feature: index output

  ExaScience/elprep#66 · Filter by author matthdsm opened on Dec 22, 2022
  2

• elprep merge: add input for intermediate files

  ExaScience/elprep#65 · Filter by author matthdsm opened on May 9, 2022

• header tag differs between runs

  ExaScience/elprep#64 · Filter by author matthdsm opened on Apr 13, 2022
  2

• Add wiki page about "creating your own sfm script"

  ExaScience/elprep#63 · Filter by author matthdsm opened on Apr 13, 2022
  3

• Proper running using sam input file?

  ExaScience/elprep#59 · Filter by author desmodus1984 opened on Jan 21, 2022
  1

• "exit status 2" error

  ExaScience/elprep#57 · Filter by author yanlolo opened on Dec 13, 2021
  2

• Variant calling using sfm does not adhere to thread limit

  ExaScience/elprep#56 · Filter by author matthdsm opened on Oct 21, 2021
  13

• [RFE] haplotypecaller: support for custom GVCF GQ slices

  ExaScience/elprep#52 · Filter by author ntm opened on Jun 30, 2021
  1

• sfm --haplotypecaller introduces duplicate lines in BAM

  ExaScience/elprep#51 · Filter by author ntm opened on Jun 30, 2021
  2

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

  ExaScience/elprep#49 · Filter by author desmodus1984 opened on Jun 6, 2021
  7

• Converting a dbsnp vcf to elsites uses a lot of resources

  ExaScience/elprep#45 · Filter by author ghost opened on Mar 15, 2021
  3

• Estimate RAM usage based on input filesize

  ExaScience/elprep#44 · Filter by author matthdsm opened on Mar 10, 2021
  14

• UMI's and duplicate marking

  ExaScience/elprep#38 · Filter by author matthdsm opened on Sep 3, 2020
  1