Comments (1)
Hi Sandy,
The issue is that the reference used for the tests must match the reference used for the alignment stored in BAM format. For the tests, this reference is compatible: http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta
You'll need to make a bwa reference (bwa index) and a samtools faidx reference.
Sorry for the confusion!
-Adam
from bamsurgeon.
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