This dataset contains small BAMs and FASTQs overlapping reasonably high-confidence variants from a patient with high quality whole genome sequencing. This can be used to measure sensitivity.
The data was derived from the guacamole cancer-wgs1 test data, which came from an australian ovarian cancer study (AOCS) patient. It contains reads overlapping ~320 called variants that were published with this dataset. The AOCS uses their own pipeline: https://sourceforge.net/projects/adamajava/
The published calls are in published_calls.csv in varlens format. These are mostly only the calls that were validated using an orthogonal method, although the details of the validation are not clear. Many other calls were made for this patient that were not attempted for validation and are not included here. Note this is whole genome sequencing.
Reads overlapping the selected variants were extracted from the original BAM (aligned by the AOCS project) and written to the small BAMs included here.
There are two tumor samples (primary and recurrence) and one normal sample. The published calls are a union of calls for both. It would probably be reasonable to just merge the primary.fastq and recurrence.fastq into one file and use that as the tumor sample. Or could call separately on each and merge. I created a merged fastq for by running:
zcat primary.fastq.gz recurrence.fastq.gz | gzip - > tumor_combined.fastq.gz
The original AOCS data was aligned to a nonstandard reference that seems to be b37 but with "chr" prefixes (but is not hg19 since mitochondria and some other contigs are named as in b37). This is an issue if we want to use this data to run from the BAM file. Running variant calling using these BAMs against hg19 may work though, if we ignore mitochondrial variants.
FASTQs were generated from the BAMs using this
bam2fastq tool with --all-to-stdout
option. However, read mates were lost, so it is possible that some reads in
these FASTQs will not align to their correct locus.
mkdir downloaded
wget https://www.dropbox.com/sh/naqgsi744z9ccqp/AADMEoLnHPupbXhLwHOz8MyDa?dl=1 -O downloaded/downloaded.zip
unzip downloaded/downloaded.zip -d downloaded/