Issues

• Segmentation fault

  amplab/snap#176 · Filter by author jhaezebr opened on Sep 24, 2026
  1

• Slaw bashi

  amplab/snap#175 · Filter by author safinkurdi34-droid opened on Jun 28, 2026
  1

• unit_tests binary crashes on sparc64 due to unaligned access (Bus error)

  amplab/snap#173 · Filter by author glaubitz opened on Sep 13, 2025

• Error: snap-aligner output multiple alignments

  amplab/snap#170 · Filter by author yi1873 opened on Apr 17, 2025
  4

• Extend Alt contigs option to allow mapping to two haplotypes genomes.

  amplab/snap#169 · Filter by author ghuls opened on Dec 12, 2023

• Feature request: name sort output

  amplab/snap#166 · Filter by author matthdsm opened on Apr 5, 2023

• mapping HiC read

  amplab/snap#165 · Filter by author yangfangyuan0102 opened on Feb 25, 2023

• bug (?): unexpected results with enforced interval size greater than default

  amplab/snap#162 · Filter by author eboyden opened on Oct 15, 2022
  4

• feature request: print LB/PL/PU/SM tags only in @RG header line

  amplab/snap#159 · Filter by author eboyden opened on Oct 3, 2022

• Feature request: markduplicate metrics and settings

  amplab/snap#158 · Filter by author matthdsm opened on Aug 25, 2022

• Indel calling

  amplab/snap#154 · Filter by author kokyriakidis opened on May 31, 2022
  3

• feature request: option to mark optical duplicates only

  amplab/snap#147 · Filter by author eboyden opened on Jan 6, 2022
  1

• Duplicate marking produces malformed QS tags in SAM output

  amplab/snap#145 · Filter by author eboyden opened on Jan 6, 2022
  3

  

• better handling of complex indel situations

  amplab/snap#143 · Filter by author bwlang opened on Dec 27, 2021
  3

• Original fastq order

  amplab/snap#127 · Filter by author jkbonfield opened on Nov 11, 2020
  2

• -F option yielding incongruous output

  amplab/snap#119 · Filter by author cxr5298 opened on Feb 25, 2019

• Test failure on ppc64 and sparc64

  amplab/snap#112 · Filter by author tillea opened on Dec 21, 2017

• Test suite failure on ppc64 and sparc64 architectures

  amplab/snap#110 · Filter by author tillea opened on Dec 20, 2017

• Public docker image?

  amplab/snap#101 · Filter by author sminot opened on Jul 19, 2017
  2

• 'SNAPCommand exit' doesn't when previous job killed.

  amplab/snap#90 · Filter by author taltman opened on May 22, 2017

• Typo in Makefile for building snapxl

  amplab/snap#89 · Filter by author taltman opened on May 22, 2017

• Error message about long reads needs to be updated

  amplab/snap#88 · Filter by author taltman opened on May 22, 2017

• can you help explain the question about the RAM used by snap

  amplab/snap#86 · Filter by author wangzhenkeep opened on Mar 29, 2017

• Build requires 188 GB of memory (fortunately not used, just allocated)

  amplab/snap#82 · Filter by author tillea opened on Jan 30, 2017
  2

• SNAP crashes when it tries to generate a BAM file with > 2GB header

  amplab/snap#76 · Filter by author bolosky opened on Aug 18, 2016