From: Sarah Wait Zaranek Date: Fri, 22 May 2020 13:11:22 +0000 (+0000) Subject: Adding yml files for gathering and intervals X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/322e4a0a20e0c349d2a18f57914239ee81e1eaef Adding yml files for gathering and intervals Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- diff --git a/yml/gather-vcf.yml b/yml/gather-vcf.yml new file mode 100644 index 0000000..779a97c --- /dev/null +++ b/yml/gather-vcf.yml @@ -0,0 +1,17 @@ +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa +sample: ERR1726424 +gvcflist: + class: File + location: /data-sdd/pgp/arvados-tutorial/src/variantcalling/sample-files.list +gvcf1: + class: File + location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz + +gvcf2: + class: File + location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf_10.gz + + + diff --git a/yml/gather-vcf2.yml b/yml/gather-vcf2.yml new file mode 100644 index 0000000..ce9852f --- /dev/null +++ b/yml/gather-vcf2.yml @@ -0,0 +1,13 @@ +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa +sample: ERR1726424 +gvcf1: + class: File + location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz + +gvcf2: + class: File + location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf_10.gz + + diff --git a/yml/gatk-applyBQSR.yml b/yml/gatk-applyBQSR.yml new file mode 100644 index 0000000..0241acd --- /dev/null +++ b/yml/gatk-applyBQSR.yml @@ -0,0 +1,13 @@ +bam: + class: File + location: keep:79407f4f0d46a44fcc9c377461ee85fc+53752/marked_dupsERR1726424.sorted.bam + +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa + +sample: ERR1726424 + +recaltable: + class: File + location: keep:fdce030a5036edb9b821222e316ee706+143/ERR1726424_recal_data.table diff --git a/yml/gatk-haplotypecaller-with-interval.yml b/yml/gatk-haplotypecaller-with-interval.yml new file mode 100644 index 0000000..4c42573 --- /dev/null +++ b/yml/gatk-haplotypecaller-with-interval.yml @@ -0,0 +1,10 @@ +bam: + class: File + location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa +intervallist: + class: File + location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list +sample: ERR1726424 diff --git a/yml/gatk-splitintervals.yml b/yml/gatk-splitintervals.yml new file mode 100644 index 0000000..68dbcc4 --- /dev/null +++ b/yml/gatk-splitintervals.yml @@ -0,0 +1,7 @@ +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa + +sample: ERR1726424 + +scattercount: "32" diff --git a/yml/gatk-wf-with-interval.yml b/yml/gatk-wf-with-interval.yml new file mode 100644 index 0000000..5761d1d --- /dev/null +++ b/yml/gatk-wf-with-interval.yml @@ -0,0 +1,13 @@ +bam: + class: File + location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa +intervallist: + class: File + location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list +sample: ERR1726424 +knownsites1: + class: File + location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz diff --git a/yml/scatter-gatk-wf-with-interval.yml b/yml/scatter-gatk-wf-with-interval.yml new file mode 100644 index 0000000..4909ce2 --- /dev/null +++ b/yml/scatter-gatk-wf-with-interval.yml @@ -0,0 +1,11 @@ +bam: + class: File + location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam +reference: + class: File + location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa +sample: ERR1726424 +scattercount: '32' +knownsites1: + class: File + location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz