initial commit

README.md

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+[![Binder](https://binder.pangeo.io/badge_logo.svg)](https://binder.pangeo.io/v2/gh/ngs-docs/2022-ggg-201b-variant-calling/stable?urlpath=rstudio)

Snakefile

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+# default rule that tells snakemake to create the .vcf file if
+# it is not run with any specific rule or file request.
+rule all:
+    input:
+        "SRR2584857_1.ecoli-rel606.vcf"
+
+rule download_data:
+    conda: "env-wget.yml"
+    output: "SRR2584857_1.fastq.gz"
+    shell: """
+        wget https://osf.io/4rdza/download -O {output}
+    """
+
+rule download_genome:
+    conda: "env-wget.yml"
+    output: "ecoli-rel606.fa.gz"
+    shell:
+        "wget https://osf.io/8sm92/download -O {output}"
+
+rule map_reads:
+    conda: "env-minimap.yml"
+    input: ref="ecoli-rel606.fa.gz", reads="SRR2584857_1.fastq.gz"
+    output: "SRR2584857_1.ecoli-rel606.sam"
+    shell: """
+        minimap2 -ax sr {input.ref} {input.reads} > {output}
+    """
+
+rule sam_to_bam:
+    conda: "env-minimap.yml"
+    input: "SRR2584857_1.ecoli-rel606.sam"
+    output: "SRR2584857_1.ecoli-rel606.bam"
+    shell: """
+        samtools view -b -F 4 {input} > {output}
+     """
+
+rule sort_bam:
+    conda: "env-minimap.yml"
+    input: "SRR2584857_1.ecoli-rel606.bam"
+    output: "SRR2584857_1.ecoli-rel606.bam.sorted"
+    shell: """
+        samtools sort {input} > {output}
+    """
+
+rule call_variants:
+    conda: "env-bcftools.yml"
+    input:
+        ref="ecoli-rel606.fa.gz",
+        bamsort="SRR2584857_1.ecoli-rel606.bam.sorted"
+    output:
+        refout="ecoli-rel606.fa",
+        pileup="SRR2584857_1.ecoli-rel606.pileup",
+        bcf="SRR2584857_1.ecoli-rel606.bcf",
+        vcf="SRR2584857_1.ecoli-rel606.vcf"
+    shell: """
+        gunzip -c {input.ref} > {output.refout}
+        bcftools mpileup -Ou -f {output.refout} {input.bamsort} > {output.pileup}
+        bcftools call -mv -Ob {output.pileup} -o {output.bcf}
+        bcftools view {output.bcf} > {output.vcf}
+    """

env-bcftools.yml

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+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bcftools=1.11
+  - samtools

env-minimap.yml

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+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - minimap2=2.17
+  - samtools=1.10

env-wget.yml

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+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - wget

environment.yml

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+name: vc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-base=3.6
+  - snakemake-minimal=5.30.1
+  - wget
+  - samtools=1.10