Hi,
setting of the reference allele in the vcf fails (informatively, thank you for that) in almost all environments.
The issue is at
|
cmdStream << "/odinn/users/snaedisk/bin/crop_fasta /odinn/data/reference/Homo_sapiens-deCODE-hg38/Sequence/WholeGenomeFasta/genome.fa " << marker.chrom << ":" << toCString(str) << "-" << marker.end; |
A simple fix would be to use samtools faidx $REF_PATH region. The environment variable REF_PATH is (should be) standard.
Hi,
setting of the reference allele in the vcf fails (informatively, thank you for that) in almost all environments.
The issue is at
popSTR/msGenotyper.cpp
Line 549 in 3a5ca74
A simple fix would be to use
samtools faidx $REF_PATH region. The environment variable REF_PATH is (should be) standard.