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Snakefile-Genetic
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Snakefile-Genetic
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# Settings for data
REGIONS = ['ch03.60Mx', 'ch04.71Mx', 'ch05.56Mx']
REFNAME = 'StSOLv1.1'
COMPLEXITY_LEVELS = [0, 2]
WINDOW_SIZES = [250]
CUTOFFS = [0]
SAMPLESIZES = ['0.25', '0.5']
PROGSAMPLES = ['150', '125', '100', '75', '60', '50', '40', '30', '25', '20', '15']
RUNSPERSIZE = 10
SAMPLE = 'Altus_470bp'
# Path to data
PARENTPATH = '/srv/homes/schrinner/data/geneticphasing/parents/'
PROGENYPATH = '/srv/homes/schrinner/data/geneticphasing/progeny/'
CCSPATH = '/srv/homes/schrinner/data/geneticphasing/ccs-reads/'
OUTPUTPATH = 'output/'
CSVPATH = 'csv/'
PEDFILE = '/srv/homes/schrinner/data/geneticphasing/peds/ped.txt'
PEDPREFIX = '/srv/homes/schrinner/data/geneticphasing/peds/ped'
READPATH = '/srv/homes/schrinner/data/geneticphasing/parents/aligned_reads/'
REFPATH = '/srv/homes/schrinner/data/geneticphasing/reference/'
START, END, CHRNAME = dict(), dict(), dict()
START['03'] = '60269000'
END['03'] = '60504000'
CHRNAME['03'] = 'ch03'
START['04'] = '71586000'
END['04'] = '71947000'
CHRNAME['04'] = 'ch04'
START['05'] = '56711000'
END['05'] = '57066000'
CHRNAME['05'] = 'ch05'
rule all:
input:
expand('{}{{region}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.new14.vcf'.format(OUTPUTPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS),
expand('{}{{region}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.sub{{subsize}}-{{run}}.new14.vcf'.format(OUTPUTPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS, subsize=PROGSAMPLES, run=range(RUNSPERSIZE)),
expand('{}{{region}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.sub{{subsize}}-{{run}}.new14.tsv'.format(CSVPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS, subsize=PROGSAMPLES, run=range(RUNSPERSIZE)),
expand('{}{{region}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.sub193-1.new14.tsv'.format(CSVPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS),
expand('{}{{region}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.avg.csv'.format(CSVPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS),
expand('{}{{region}}-{{samplesize}}.genetic.altus.c{{complexity}}.w{{window}}.cut{{cutoff}}.new14.tsv'.format(CSVPATH), region=REGIONS, complexity=COMPLEXITY_LEVELS, window=WINDOW_SIZES, cutoff=CUTOFFS, samplesize=SAMPLESIZES),
rule genetic_phase:
input:
parent=PARENTPATH+'ch{chr, \d+}.{region, \d+Mx}{samplesize, [\d\.-]*}.parents.decluttered.vcf',
progeny=PROGENYPATH+'ch{chr, \d+}.{region, \d+Mx}.progeny.decluttered.vcf.gz',
pedfile=PEDFILE
output:
OUTPUTPATH+'ch{chr, \d+}.{region, \d+Mx}{samplesize, [\d\.-]*}.genetic.altus.c{complexity}.w{window}.cut{cutoff,\d+}.new14.vcf'
shell:
'whatshap polyphasegenetic {input.parent} {input.pedfile} -P {input.progeny} -p 4 -o {output} --sample Altus_470bp -C {wildcards.complexity} --scoring-window {wildcards.window} --ratio-cutoff {wildcards.cutoff} --distrust-parent-genotypes'
rule genetic_phase_subsampled:
input:
parent=PARENTPATH+'{region}.parents.decluttered.vcf',
progeny=PROGENYPATH+'{region}.progeny.decluttered.vcf.gz',
pedfile=PEDPREFIX+'{subsize}_{run}.txt'
output:
OUTPUTPATH+'{region}.genetic.altus.c{complexity}.w{window}.cut{cutoff,\d+}.sub{subsize}-{run}.new14.vcf'
log:
OUTPUTPATH+'{region}.genetic.altus.c{complexity}.w{window}.cut{cutoff}.sub{subsize}-{run}.new14.log'
shell:
'whatshap polyphasegenetic {input.parent} {input.pedfile} -P {input.progeny} -p 4 -o {output} --sample Altus_470bp -C {wildcards.complexity} --scoring-window {wildcards.window} --ratio-cutoff {wildcards.cutoff} --distrust-parent-genotypes 2> {log}'
rule compare:
input:
phase=OUTPUTPATH+'ch{chr, \d+}.{region}.genetic.altus.{suffix}.vcf',
truth='ch{chr, \d+}/ch{chr, \d+}.combined.vcf.gz'
output:
CSVPATH+'ch{chr, \d+}.{region}.genetic.altus.{suffix}.tsv'
shell:
'whatshap compare {input.phase} {input.truth} -p 4 --tsv-pairwise {output}'
rule create_csv:
input:
expand(CSVPATH+'{{region}}.genetic.altus.c{{complexity}}.{{options}}.sub{subsize}-{run}.new14.tsv', subsize=PROGSAMPLES, run=range(RUNSPERSIZE)),
expand(CSVPATH+'{{region}}.genetic.altus.c{{complexity}}.{{options}}.sub{subsize}-{run}.new14.tsv', subsize=[193], run=[1])
output:
CSVPATH+'{region}.genetic.altus.c{complexity}.{options}.avg.csv'
shell:
'python3 compare_samplescaling.py {CSVPATH} {output} {wildcards.region} {wildcards.complexity}'
rule cut_vcf:
input:
vcf=PARENTPATH+'ch{chr, \d+}{samplesize, [\d\.-]*}.parents.vcf.gz',
index=PARENTPATH+'ch{chr, \d+}{samplesize, [\d\.-]*}.parents.vcf.gz.csi'
output:
PARENTPATH+'ch{chr, \d+}.{region, \d+Mx}{samplesize, [\d\.-]*}.parents.decluttered.vcf'
run:
ch = CHRNAME[wildcards.chr]
start = START[wildcards.chr]
end = END[wildcards.chr]
#shell('bgzip < {input.vcf} > {input.vcf}.gz')
#shell('bcftools index {input}.gz')
shell('bcftools view {input} -O v -o {output}.cluttered.vcf -r {REFNAME}{ch}:{start}-{end}')
shell('python3 declutter_vcf.py {output}.cluttered.vcf {output}')
#shell('rm {input}.gz')
#shell('rm {input}.gz.csi')
shell('rm {output}.cluttered.vcf')
# Creating downsampled files
rule extract_chromosome:
input:
bam='{prefix}.srt.bam',
bai='{prefix}.srt.bam.bai'
output:
bam='{prefix}.srt.ch{chr, \d+}.bam',
bai='{prefix}.srt.ch{chr, \d+}.bam.bai'
run:
shell("sambamba view -f sam -h -o {output.bam}.sam {input.bam} {REFNAME}ch{wildcards.chr}:1-90000000")
shell("sed -i '/chloroplast/d' {output.bam}.sam | sed -i '/mitochondrial/d' {output.bam}.sam")
shell("sambamba view -f bam -h -S -o {output.bam} {output.bam}.sam")
shell("rm {output.bam}.sam")
rule downsample_bam:
input:
bam='{prefix}.srt.ch{chr}.bam',
bai='{prefix}.srt.ch{chr}.bam.bai'
output:
bam='{prefix}.srt.ch{chr}-{percentage, [\.\d]+}.unsorted.bam'
run:
shell('gatk DownsampleSam -I {input.bam} -O {output.bam} -P {wildcards.percentage}')
rule sort_bam:
input:
bam='{prefix}.srt.ch{chr}-{percentage, -*\d*\.*\d*}.unsorted.bam'
output:
bam='{prefix}.srt.ch{chr}-{percentage, -*\d*\.*\d*}.bam',
bai='{prefix}.srt.ch{chr}-{percentage, -*\d*\.*\d*}.bam.bai'
shell:
'sambamba sort -o {output.bam} {input.bam}'
rule call_variants:
input:
bam=READPATH+'{prefix}.bam',
bai=READPATH+'{prefix}.bam.bai',
ref=REFPATH+'SolyntusV1.1.fasta',
fai=REFPATH+'SolyntusV1.1.fasta.fai',
dict=REFPATH+'SolyntusV1.1.dict'
output:
gvcf=PARENTPATH+'{prefix}.bam.g.vcf.gz'
shell:
'gatk --java-options "-Xmx4g" HaplotypeCaller --native-pair-hmm-threads 4 -R {input.ref} -I {input.bam} -O {output.gvcf} -ERC GVCF --sample-ploidy 4'
rule merge_gvcf:
input:
altus=PARENTPATH+'Altus_470bp.SolyntusV1.1_CPMT.srt.ch{chr, \d+}-{percentage}.bam.g.vcf.gz',
colomba=PARENTPATH+'Colomba_470bp.SolyntusV1.1_CPMT.srt.ch{chr, \d+}-{percentage}.bam.g.vcf.gz',
ref=REFPATH+'SolyntusV1.1.fasta',
fai=REFPATH+'SolyntusV1.1.fasta.fai',
dict=REFPATH+'SolyntusV1.1.dict'
output:
vcf=PARENTPATH+'AC_parents.ch{chr, \d+}-{percentage}.vcf'
run:
shell('mkdir {output.vcf}.temp -p')
shell('gatk --java-options "-Xmx100g -Xms100g" GenomicsDBImport --variant {input.altus} --variant {input.colomba} --genomicsdb-workspace-path {output.vcf}.genomicsdb --tmp-dir {output.vcf}.temp --reader-threads 10 -L StSOLv1.1ch{wildcards.chr}')
shell('gatk --java-options "-Xmx40g" GenotypeGVCFs -R {input.ref} -V gendb://{output.vcf}.genomicsdb -O {output.vcf}')
rule compress_vcf:
input:
PARENTPATH+'AC_parents.ch{chr, \d+}-{suffix}.vcf'
output:
vcf=PARENTPATH+'ch{chr, \d+}-{suffix}.parents.vcf.gz'
run:
shell('bgzip < {input} -o {output.vcf}')
rule index_vcf:
input:
'{prefix}.vcf.gz'
output:
'{prefix}.vcf.gz.csi'
run:
shell('bcftools index {input}')