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Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2378 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-12-16 20:44:30 +00:00
parent f5e547ed6e
commit 4e7e0432a2
2 changed files with 24 additions and 23 deletions
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2
python/CoverageEval.py
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@ -221,7 +221,7 @@ def stats_from_hist(options, depth_hist_filename, stats_filename, variant_eval_d
hist = [] hist = []
hist_gen = FlatFileTable.record_generator(depth_hist_filename, sep=" ", skip_n_lines=9) hist_gen = FlatFileTable.record_generator(depth_hist_filename, sep=" ", skip_until_regex_line = "^depth count freq")
for index, record in enumerate(hist_gen): for index, record in enumerate(hist_gen):
assert int(record["depth"]) == index assert int(record["depth"]) == index
hist.append(int(record["count"])) hist.append(int(record["count"]))

43
python/CoverageMeta.py
View File

@ -44,9 +44,13 @@ def process_bam(bam_file):
sys.exit("Expected to find "+hapmapchip_file+" but it's not around") sys.exit("Expected to find "+hapmapchip_file+" but it's not around")
else: else:
# Config for pilot 3 # Config for pilot 3 Broad data
ref = " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" #ref = " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
intervals_file = "/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.targets.interval_list" #intervals_file = "/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.targets.interval_list"
# Config for pilot 3 DCC data (12/16/09 r. 2375)
ref = " -R /broad/1KG/reference/human_b36_both.fasta"
intervals_file = "/humgen/gsa-scr1/GATK_Data/thousand_genomes_alpha_redesign.targets.b36.interval_list"
# Assure that BAM index exists # Assure that BAM index exists
bam_index_file = output_basepath+".bam.bai" bam_index_file = output_basepath+".bam.bai"
@ -54,13 +58,13 @@ def process_bam(bam_file):
Cmd = "samtools index "+bam_file Cmd = "samtools index "+bam_file
cmd(Cmd, die_on_fail = True) cmd(Cmd, die_on_fail = True)
# Run SSG calls # Run UnifiedGenotyper calls
ssg_outfile = output_basepath+".SSG.calls" vcf_outfile = output_basepath+".calls.vcf"
if not exists_and_non_zero(ssg_outfile): if not exists_and_non_zero(vcf_outfile):
print "Running SingleSampleGenotyper" print "Running UnifiedGenotyper"
Cmd = gatk_exe + ref + " -T SingleSampleGenotyper"+\ Cmd = gatk_exe + ref + " -T UnifiedGenotyper"+\
" -I "+bam_file+\ " -I "+bam_file+\
" -varout "+ssg_outfile+\ " -varout "+vcf_outfile+\
" -L "+intervals_file+\ " -L "+intervals_file+\
" -fmq0 -l INFO " " -fmq0 -l INFO "
#" --genotype -lod 5" #" --genotype -lod 5"
@ -68,22 +72,18 @@ def process_bam(bam_file):
#+interval_string+\ #+interval_string+\
cmd(Cmd, die_on_fail=True) cmd(Cmd, die_on_fail=True)
# Run VariantEval on SSG calls # Run VariantEval on UnifiedGenotyper calls
varianteval_outdir = output_basepath+".VariantEval" varianteval_outfile = output_basepath+".varianteval"
varianteval_outbase = output_basepath+".VariantEval/"+output_basepath
varianteval_outfile = output_basepath+".VariantEval/"+output_basepath #+".all.genotype_concordance"
if not exists_and_non_zero(varianteval_outfile): if not exists_and_non_zero(varianteval_outfile):
print "Running VariantEval with output to "+varianteval_outbase print "Running VariantEval with output to "+varianteval_outfile
if not os.path.exists(varianteval_outdir):
os.mkdir(varianteval_outdir)
Cmd = gatk_exe + ref + " -T VariantEval"+\ Cmd = gatk_exe + ref + " -T VariantEval"+\
" -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\ " -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\
" -B eval,Variants,"+ssg_outfile+\ " -B eval,VCF,"+ssg_outfile+\
" -o "+varianteval_outbase+\ " -o "+varianteval_outfile+\
" -L "+intervals_file+\ " -L "+intervals_file+\
" -G -V"+\
" --evalContainsGenotypes"+\ " --evalContainsGenotypes"+\
" -minConfidenceScore 5"+\ " -minPhredConfidenceScore 150"+\
" -fmq0 -l INFO" " -fmq0 -l INFO"
if using_hapmapchip: if using_hapmapchip:
Cmd = Cmd + " -hc "+hapmapchip_file Cmd = Cmd + " -hc "+hapmapchip_file
@ -94,10 +94,11 @@ def process_bam(bam_file):
hist_outfile = output_basepath+".hapmap.coverage_hist" hist_outfile = output_basepath+".hapmap.coverage_hist"
if not exists_and_non_zero(hist_outfile): if not exists_and_non_zero(hist_outfile):
print "Running CoverageHist on "+bam_file print "Running CoverageHist on "+bam_file
Cmd = gatk_exe + ref + " -T CoverageHistogram"+\ Cmd = gatk_exe + ref + " -T DepthOfCoverage"+\
" -I "+bam_file+\ " -I "+bam_file+\
" -o "+hist_outfile+\ " -o "+hist_outfile+\
" -L "+intervals_file+\ " -L "+intervals_file+\
" -histogram --suppressLocusPrinting"+\
" -fmq0 -l INFO" " -fmq0 -l INFO"
cmd(Cmd, die_on_fail=True)#,"gsa", output_basepath) cmd(Cmd, die_on_fail=True)#,"gsa", output_basepath)