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SouthGreenPlatform / VcfHunter

VcfExplorer regroups several programs which principal aims are to map DNA and RNAseq data onto reference genome sequence, perform variant calling, manipulate vcf files, perform chromosome painting of accessions based on the contribution of ancestral groups, select marker for genetic map analysis and perform pairwise chromosome linkage of ordered markers.
GNU General Public License v3.0
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Error in step A: read group line contained literal <tab> #3

Open sanderdebacker opened 2 years ago

sanderdebacker commented 2 years ago

When running the process_reseq_1.0.py script, the following error occurs:

Line : 677 - Error in step A (bwa-mem): [E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \t

Does anyone know whatever causes this error and how to resolve it?

guiguimartin commented 2 years ago

Maybe this is linked to a new version of BWA installed. Which version have you installed? On our computer we use: bwa/0.7.15 and it works fine.

sanderdebacker commented 2 years ago

Solution that worked for me (with bwa-0.7.17).

Replace line 657 in the /utilsSR/utilsSR.py script to: rg_tag = '@RG"\\t"ID:'+ACC_ID+'"\\t"SM:'+ACC_ID+'"\\t"LB:'+ACC_ID+'"\\t"PU:whatever"\\t"PL:ILLUMINA'

Original: rg_tag = '@RG"\t"ID:'+ACC_ID+'"\t"SM:'+ACC_ID+'"\t"LB:'+ACC_ID+'"\t"PU:whatever"\t"PL:ILLUMINA'