adds scripts

.gitignore

@@ -1,3 +1,13 @@
 .DS_Store
 site
 env/
+data/
+.cache/
+.bash_history
+.bashrc
+.conda/
+.config/
+.lesshst
+.local/
+.profile
+extensions/

Docker/environment.yml

@@ -8,5 +8,5 @@ dependencies:
   - snpeff>=5.0
   - gatk4=4.5
   - r-base
-  - cnvkit
+  - cnvkit>=0.9.10
   - bcftools

scripts/01_download_data.sh

@@ -59,4 +59,6 @@ bcftools view -Oz -r chr6,chr17 af-only-gnomad.hg38.vcf.gz > af-only-gnomad.hg38
 bcftools index --tbi af-only-gnomad.hg38.subset.vcf.gz
 
 bcftools view -Oz -r chr6,chr17 1000g_pon.hg38.vcf.gz > 1000g_pon.hg38.subset.vcf.gz
-bcftools index --tbi 1000g_pon.hg38.subset.vcf.gz
+bcftools index --tbi 1000g_pon.hg38.subset.vcf.gz
+
+wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz

scripts/07_get_pileups.sh

@@ -8,7 +8,7 @@ for sample in tumor normal
 do
     gatk GetPileupSummaries \
     -I "$ALIGNDIR"/"$sample".rg.md.bam \
-    -V "$RESOURCEDIR"/af-only-gnomad.hg38.vcf.gz \
-    -L "$RESOURCEDIR"/af-only-gnomad.hg38.vcf.gz \
+    -V "$RESOURCEDIR"/af-only-gnomad.hg38.subset.vcf.gz \
+    -L "$RESOURCEDIR"/af-only-gnomad.hg38.subset.vcf.gz \
     -O "$VARIANTDIR"/"$sample".pileups.table
 done

scripts/08_calculate_contamination.sh

@@ -7,4 +7,4 @@ RESOURCEDIR=/config/data/resources
 gatk CalculateContamination \
 -I "$VARIANTDIR"/tumor.pileups.table \
 -matched "$VARIANTDIR"/normal.pileups.table \
--O "$VARIANTDIR"/ontamination.table
+-O "$VARIANTDIR"/contamination.table

scripts/09_filter_variants.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+ALIGNDIR=/config/data/alignments
+REFDIR=/config/data/reference
+RESOURCEDIR=/config/data/resources
+VARIANTDIR=/config/data/variants
+
+gatk FilterMutectCalls \
+-R "$REFDIR"/ref_genome.fa \
+-V "$VARIANTDIR"/somatic.vcf.gz \
+-O "$VARIANTDIR"/somatic.filtered.vcf.gz

scripts/10_run_cnvkit.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+ALIGNDIR=/config/data/alignments
+REFDIR=/config/data/reference
+RESOURCEDIR=/config/data/resources
+VARIANTDIR=/config/data/variants
+
+cnvkit.py batch "$ALIGNDIR"/tumor.rg.md.bam \
+--normal "$ALIGNDIR"/normal.rg.md.bam \
+--targets "$REFDIR"/exome_regions.bed.interval_list \
+--fasta "$REFDIR"/ref_genome.fa \
+--annotate "$RESOURCEDIR"/refFlat.txt.gz \
+--output-reference "$VARIANTDIR"/reference.cnn \
+--output-dir "$VARIANTDIR"/cnvkit/