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=== allelic imbalance ===
=== allelic imbalance ===
A statistic developed by Dr. Tom Blackwell [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_Based_Allele_Balance allelic imbalance].
A statistic developed by Dr. Tom Blackwell [http://genome.sph.umich.edu/wiki/Genotype_Likelihood_Based_Allele_Balance allelic imbalance].
=== 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).
=== strand bias filter ===
=== total depth filter ===
=== total depth filter ===
=== flanking sequence 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.
We recommend excluding sites with >0.1% flanking 10-mer frequency among candidate sites. samtools calmd -br performs this base quality re-calibration.
== Questions and Comments? ==
== Questions and Comments? ==
Email [mailto:yunli@med.unc.edu Yun Li].
Email [mailto:yunli@med.unc.edu Yun Li].
