From Genome Analysis Wiki
=== allelic imbalance ===
A statistic developed by Dr. Tom Blackwell [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_Based_Allele_Balance allelic imbalance].
=== total depth filter ===
=== flanking sequence filter ===
We recommend excluding sites with >0.1% flanking 10-mer frequency among candidate sites. samtools calmd -br performs this base quality re-calibration.
=== indel filter ===
We recommend distance to known indels >= 5bp. A catalog of known indels can be found at [ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/indels/ indel catalog].
=== site promotion filter ===
We recommend setting parameter -p at least >= 0.9 in step 1 (running glfMultiples).
== Questions and Comments? ==
Email [mailto:firstname.lastname@example.org Yun Li].