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Revision as of 17:20, 11 September 2021
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[[Category:libStatGen]]
[[Category:libStatGen BAM]]
== How Do I? ==
== How Do I? ==
===== Q: What is SAM/BAM? =====
* A: See: [[SAM]] and [[BAM]]. [[SAM]] also provides additional details as to what is a CIGAR, QUALITY, and TAG.
===== Q: Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference base for a given read position? =====
===== Q: Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference base for a given read position? =====
* A: Use [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|CigarRoller::getQueryIndex & CigarRoller::getRefOffset]]
* A: Use [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Cigar::getQueryIndex & Cigar::getRefOffset]]
===== Q: Read only portions of a sorted & indexed BAM file that fall within a specified region? =====
===== Q: Read only portions of a sorted & indexed BAM file that fall within a specified region? =====
===== Q: Get additional information on this library? =====
===== Q: Get additional information on this library? =====
* A: Email me, Mary Kate, at mktrost@umich.edu.
* A: If you have any questions or comments, please raise issue in [https://github.com/statgen/ our GitHub repositories].
