jo-mc

is $GENOME_REFERENCE the same as Homo_sapiens_assembly38.fasta ? i guess so, then in reseq you are using normal.recal.bam (not sorted?) is this the sorted bam output ? $PREFIX.sorted.bam .......you should be...

No that should be ok, Check the RNAME order in the bam header against the reference contig names. >samtools view -H normal.recal.bam | less HLA-DRB1*16:02:01 is the last conitg in...

Hi, I ran a test with illumina reads aligned to Homo_sapiens_assembly38.fasta, generated a bam and ran reseq and I get the same error? Not sure why the code looks ok?...

If you use the "ucsc no alt grc38 reference" it looks like it is working, but I have not done a full test, [GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz] (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz) Location: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ The "analysis set"...

I tried a few variations and still get errors. Maybe move to something else?