Eris is a program for calculating sample concordance between BAM/CRAM alignment files and SNP array files in birdseed format. Also provided are scripts for converting array files for some common SNP chips (such as Fluidigm SNPTrace and OmniExpress1.0) into the birdseed format.

The output report files provide an estimated level of contamination between a given BAM and its specific array file and a sorted table of estimated concordance for each array file in a given directory.

Eris can also be run with the -g flag to create a file containing genotypes at each probelist site from the given BAM. These files are much smaller than the BAM itself and can be used with the -i flag to run concordance in place of the BAM.

Contributors: Adam English, Adam Mansfield, Shruthi Ambreth, Jeffrey Reid

Requires Python 3 and pysam 8.4+.

Some of the conversion scripts require Perl 5.

• Use provided scripts (under array_kits/) to convert array files into birdseed format.

• Move all birdseed files into one directory.

• Ensure the BAM/CRAM file you will use is indexed (such as with samtools index).

• Then run:

python3 Eris.py -b BAM -a ARRAY_DIR -A SELF_ARRAY -p PROBELIST -o OUTFILE

• For example:

python3 Eris.py -b NA12878.bam -a /path/to/birdseeds_dir \
      -A /path/to/birdseeds_dir/NA12878.birdseed -o NA12878.report.txt \
      -p ../array_kits/fluidigm_37/probelist.txt

Copyright 2017 Baylor College of Medicine Human Genome Sequencing Center