Add GATK ValidateVariants

bio/gatk/validatevariants/environment.yaml

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+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - gatk4 ==4.1.4.1
+  - snakemake-wrapper-utils ==0.1.3

bio/gatk/validatevariants/meta.yaml

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+name: GATK ValidateVariants
+description: Interleave two paired-end FASTA/Q files
+url: https://gatk.broadinstitute.org/hc/en-us/articles/360037057272-ValidateVariants
+authors:
+  - Graeme Ford
+input:
+  vcf: VCF file to be validated
+output:
+  - VCF output file
+params:
+  extra: any extra commands as a string
+notes: Multiple threads can be used during compression of the output file with ``pigz``.

bio/gatk/validatevariants/test/Snakefile

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+rule vcf_spec_validation:
+    input:
+        vcf="sample.vcf",
+    output:
+        "results/sample_VALID.vcf",
+    log:
+        "results/sample_VALID.log",
+    params:
+        R="genome.fasta",
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/gatk/validatevariants"

bio/gatk/validatevariants/test/genome.dict

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+@HD	VN:1.5
+@SQ	SN:ref	LN:45	M5:7a66cae8ab14aef8d635bc80649e730b	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta
+@SQ	SN:ref2	LN:40	M5:1636753510ec27476fdd109a6684680e	UR:file:/home/johannes/scms/snakemake-wrappers/bio/picard/createsequencedictionary/test/genome.fasta

bio/gatk/validatevariants/test/genome.fasta

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+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT
+>ref2
+aggttttataaaacaattaagtctacagagcaactacgcg

bio/gatk/validatevariants/test/genome.fasta.fai

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+ref	45	5	45	46
+ref2	40	57	40	41

bio/gatk/validatevariants/test/sample.vcf

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+##fileformat=VCFv4.0
+##fileDate=20170110
+##source=pindel
+##reference=hg38
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##FORMAT=<ID=PL,Number=3,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
+ref	8	.	A	G	.	PASS	END=140434574;HOMLEN=5;HOMSEQ=AAAAA;SVLEN=35;SVTYPE=INS	GT:AD	0/0:317,6
+ref2	10	.	A	AGTTA	.	PASS	END=55238278;HOMLEN=7;HOMSEQ=CTGCCAC;SVLEN=-51;SVTYPE=DEL	GT:AD	0/0:40789,1734

bio/gatk/validatevariants/wrapper.py

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+__author__ = "Graeme Ford"
+__copyright__ = "Copyright 2021, Graeme Ford"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+extra = snakemake.params.get("extra", "")
+java_opts = get_java_opts(snakemake)
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+extra = snakemake.params.get("extra", "")
+
+
+shell(
+    "gatk "
+    "--java-options '{java_opts}' "
+    "ValidateVariants "
+    "-V {snakemake.input.vcf} "
+    "{extra} "
+    "{log} "
+    "> {output}"
+)