Issues

• Broken command in 'How to install snpArcher'

  harvardinformatics/snparcher#353 · Filter by author TymekPieszko opened on Oct 21, 2026

• Long contig auto mode may not always work

  harvardinformatics/snparcher#350 · Filter by author tsackton opened on Oct 1, 2026

• Revisit bwa mem flags: drop -M, consider -Y, fix -K for deterministic alignment

  harvardinformatics/snparcher#346 · Filter by author tsackton opened on Sep 24, 2026

• Replace GATK VariantFiltration with bcftools filter for hard filtering

  harvardinformatics/snparcher#344 · Filter by author tsackton opened on Sep 15, 2026

• GATK VariantFiltration can't use CSI-indexed raw.vcf.gz -- breaks hard filtering for long-contig genomes

  harvardinformatics/snparcher#341 · Filter by author tsackton opened on Jul 29, 2026

• clam and -t (--threads)

  harvardinformatics/snparcher#340 · Filter by author brantfaircloth opened on Jul 28, 2026
  4

  

• callable_sites rules and highly variable coverage

  harvardinformatics/snparcher#333 · Filter by author brantfaircloth opened on Jul 15, 2026
  5

• incorporating angsd into SNPArcher

  harvardinformatics/snparcher#330 · Filter by author linnea-schaefer opened on Jul 1, 2026
  1

• Error in rule bwa_mem: CalledProcessError

  harvardinformatics/snparcher#329 · Filter by author acoykendall2-coder opened on Jun 24, 2026
  3

• Add CRAM support

  enhancement
  harvardinformatics/snparcher#328 · Filter by author tsackton opened on Jun 18, 2026

• QC should fail clearly when min_depth filters out all samples

  harvardinformatics/snparcher#327 · Filter by author tsackton opened on May 28, 2026

• [discussion] snparcher CLI

  harvardinformatics/snparcher#287 · Filter by author pdimens opened on Mar 9, 2026
  6

• DB2vcf / CombineGVCFs error out with MNPs

  harvardinformatics/snparcher#219 · Filter by author shelbirussell opened on Sep 4, 2024

• restricting variant calls

  enhancementlowpriority
  harvardinformatics/snparcher#208 · Filter by author TonyKess opened on Jun 17, 2024
  3

• Add snp density visualization to QC module

  enhancementlowpriority
  harvardinformatics/snparcher#109 · Filter by author tsackton opened on Jun 5, 2023

• Automatically determine correct coverage parameters

  enhancementlowpriority
  harvardinformatics/snparcher#15 · Filter by author tsackton opened on Aug 6, 2021
  1