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Revision as of 16:08, 22 February 2012
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= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =
= Overview of the <code>indelDiscordance</code> function of <code>bamUtil</code> =
The <code>indelDiscordance</code> option on the [[bamUtil]] looks at discordance at sites on the male X chromosome.
The <code>indelDiscordance</code> option on the [[bamUtil]] looks at insertion/deletion discordance.
By default it looks only at the non-pseudoautosomal region of the X-Chromosome.
== ASSUMPTIONS/RESTRICTIONS ==
== ASSUMPTIONS/RESTRICTIONS ==
* Only works on one chromosome at a time
* Repeats are single-base only
* Skips reference positions with base 'N'
=== What is a Discordance ===
A position is considered to have a Deletion Discordance if at least 1 read has a match/mismatch AND at least 1 read has a deletion AND there are at least the "minimum depth" reads at this position.
A position is considered to have an Insertion Discordance if at least 1 read has an insertion following this position AND at least 1 read does not AND there are at least the "minimum depth" reads at this position.
= Usage =
= Usage =
