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comparison bwa_macros.xml @ 13:ceed4b724f0b 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 15:25:41 +0000
parents 6def3ba376a7
children 23e88ff6c494
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12:086ba7b646e5 13:ceed4b724f0b
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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):
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