From acb5112af6e34e0bb19d632fde6c18fe8c3e5b05 Mon Sep 17 00:00:00 2001 From: Stanley Lan Date: Mon, 26 Aug 2019 20:10:27 -0400 Subject: [PATCH 1/2] Update Readme.md --- dx_app_code/parliament2/Readme.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dx_app_code/parliament2/Readme.md b/dx_app_code/parliament2/Readme.md index 3a35baca..c5c8ed66 100644 --- a/dx_app_code/parliament2/Readme.md +++ b/dx_app_code/parliament2/Readme.md @@ -46,6 +46,8 @@ This app will output a number of files, representing the outputs of each of the ## Additional Notes +In order to take advantage of the structural variant tools used in the Parliament2 app, proper read group information is needed in the input mapping (BAM) file. Detailed format specification for Illumina BAM file can be found in https://support.illumina.com/help/BS_App_ENR_OLH_15050961/Content/Source/Informatics/BAM-Format.htm + Because the field of structural variation is relatively new and complex, we viewed placing a dependency on all individual tools completing successfully as a requirement for a successful run to be too strict. In other words, if one of these tools fails while the others succeed, the app will output the results of the tools that completed and will not itself fail. Breakseq2 may only be able to work when using the 1000 Genomes reference genome (hs37d5). For other reference genomes, you may not get Breakseq2 results. From 88fef78f385a565c8452427b878a0361794e7a45 Mon Sep 17 00:00:00 2001 From: Stanley Lan Date: Mon, 26 Aug 2019 20:13:43 -0400 Subject: [PATCH 2/2] Update Readme.md --- dx_app_code/parliament2/Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dx_app_code/parliament2/Readme.md b/dx_app_code/parliament2/Readme.md index c5c8ed66..1502c707 100644 --- a/dx_app_code/parliament2/Readme.md +++ b/dx_app_code/parliament2/Readme.md @@ -46,7 +46,7 @@ This app will output a number of files, representing the outputs of each of the ## Additional Notes -In order to take advantage of the structural variant tools used in the Parliament2 app, proper read group information is needed in the input mapping (BAM) file. Detailed format specification for Illumina BAM file can be found in https://support.illumina.com/help/BS_App_ENR_OLH_15050961/Content/Source/Informatics/BAM-Format.htm +In order to take advantage of the structural variant tools used in the Parliament2 app, proper read group information is needed in the input mapping (BAM) file. Detailed format specification for Illumina BAM file can be found in . Because the field of structural variation is relatively new and complex, we viewed placing a dependency on all individual tools completing successfully as a requirement for a successful run to be too strict. In other words, if one of these tools fails while the others succeed, the app will output the results of the tools that completed and will not itself fail.