Writing a Custom ReadFilter for the GATK, my notebook.

The GATK contains a set of predefined read filters that "filter or transfer incoming SAM/BAM data files":BadCigar
BadMate
CountingRead
DuplicateRead
FailsVendorQualityCheck
LibraryRead
MalformedRead
MappingQuality
MappingQualityUnavailable
(...)
With the help of the modular architecture of the GATK, it's possible to write a custom ReadFilter. In this post I'll write a ReadFilter that removes the

Source: YOKOFAKUN - September 21, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs