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BauerLab / ngsane

Analysis Framework for Biological Data from High Throughput Experiments
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SamVar #47

Open BauerLab opened 10 years ago

BauerLab commented 10 years ago

Samtools variant calling is not working anymore with samtools 1.1

[bam_rmdup_core] processing reference 16...
Samtools-htslib-API: bam_get_library() not yet implemented
/apps/gi/ngsane/devel_db//mods/samSNPs.sh: line 97: 1358176 Aborted                 samtools rmdup $f $OUTDIR/${n/bam/drm.bam}

This is a known issue with samtools 1.1 (https://github.com/samtools/samtools/issues/291)

BauerLab commented 10 years ago

Workaround: use older version (e.g. samtools/0.1.19) by adjusting the default set of modules used in the samvar_config.txt

MODULE_SAMVAR=$MODULE_SAMVAR" samtools/0.1.19"