From fc58fbed39baa5e41de2ccd9c0133eabd1e66c3d Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Fri, 2 Jun 2023 15:34:12 +0100 Subject: [PATCH 1/3] if a value is supplied for the parameter hs_bwa_executable, use that for non-consented human split alignment with bwa (instead of bwa_executable). This is to allow use of a different bwa_executable (e.g. bwa-mem2) for --- data/vtlib/target_nchs_alignment.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/data/vtlib/target_nchs_alignment.json b/data/vtlib/target_nchs_alignment.json index 60e19950d..977a8b220 100644 --- a/data/vtlib/target_nchs_alignment.json +++ b/data/vtlib/target_nchs_alignment.json @@ -187,6 +187,9 @@ "type":"VTFILE", "comment":"inputs: _stdin_ (bam), reference; outputs: _stdout_ (bam)", "node_prefix":"alntgt_hs_", + "subst_map":{ + "bwa_executable":{"subst":"hs_bwa_executable", "ifnull":{"subst":"bwa_executable"}} + }, "orig_name":{"subst":"alignment_vtf"}, "name":{ "subst":"alignment_vtf", From 231436e6996b1de0c3e6363b31a99275c81afe81 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Mon, 5 Jun 2023 12:20:09 +0100 Subject: [PATCH 2/3] update Changes --- Changes | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Changes b/Changes index 1af635549..c9a173282 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,8 @@ CHANGES LOG ----------- + - add hs_bwa_executable parameter to allow different bwa executables for target and nchs alignments (e.g. bwa-mem2 and bwa0_6) + 0.35.0 - replace scramble with samtools in analysis pipeline templates From f4a394f4d5f19a6d7c0d8656c9f2dcee27fe256d Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Mon, 5 Jun 2023 18:03:34 +0100 Subject: [PATCH 3/3] add optminpixeldif flag (optical distance for duplicates) to bamstreamingmarksuplicates command (biobambam markdup method) --- data/vtlib/markdup_biobambam.json | 1 + 1 file changed, 1 insertion(+) diff --git a/data/vtlib/markdup_biobambam.json b/data/vtlib/markdup_biobambam.json index f5a69f54d..018d7c801 100644 --- a/data/vtlib/markdup_biobambam.json +++ b/data/vtlib/markdup_biobambam.json @@ -46,6 +46,7 @@ {"subst":"bmd_metrics_file_flag"}, {"subst":"bmd_resetdupflag"}, {"subst":"bsmd_maxreadlen_flag","required":false,"ifnull":{"subst_constructor":{"vals":[ "maxreadlen", {"subst":"bsmd_maxreadlen_val","required":true, "ifnull":"500"} ],"postproc":{"op":"concat","pad":"="}}}}, + {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}}, {"subst":"bsmd_arbitrary_flags"} ] }