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comparison bwa_macros.xml @ 23:3fe632431b68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
author iuc
date Tue, 19 May 2020 11:29:11 -0400
parents 8d2a528a9513
children 2477830927ec
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22:01ac0a5fedc3 23:3fe632431b68
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113 One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do this directly in BWA interface using the 113 One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do this directly in BWA interface using the
114 **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID. 114 **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID.
115 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as 115 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as
116 instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify 116 instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify
117 data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller 117 data from different experiments even if they are combined in one file. Many downstream analysis tools such as variant callers (e.g., FreeBayes or Naive Variant Caller
118 present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file. 118 present in Galaxy) are aware of read groups and will automatically generate calls for each individual sample even if they are combined within a single file.
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120 **Description of read groups fields** 120 **Description of read groups fields**
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122 (from GATK FAQ webpage): 122 (from GATK FAQ webpage):
123 123