wespipeline
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wespipeline
wespipeline
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Index
A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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O
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P
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A
accession_number (wespipeline.fastq.GetFastq attribute)
(wespipeline.fastq.SraToolkitFastq attribute)
AlignProcessing (class in wespipeline.processalign)
B
bai_local_file (wespipeline.processalign.AlignProcessing attribute)
bam_local_file (wespipeline.processalign.AlignProcessing attribute)
base_dir (wespipeline.utils.GlobalParams attribute)
biallelic_block_substitutions (wespipeline.vcfanalysis.DockerVTnormalizeVCF attribute)
biallelic_clumped_variant (wespipeline.vcfanalysis.DockerVTnormalizeVCF attribute)
BIN_VERSION (wespipeline.vcf.DeepvariantDockerTask attribute)
(wespipeline.vcf.DockerGatkCallVariants attribute)
binds() (wespipeline.vcf.DeepvariantDockerTask property)
(wespipeline.vcf.DockerGatkCallVariants property)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF property)
BwaAlignFastq (class in wespipeline.align)
BwaIndex (class in wespipeline.reference)
C
command() (wespipeline.vcf.DeepvariantDockerTask property)
(wespipeline.vcf.DockerGatkCallVariants property)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF property)
compressed (wespipeline.fastq.GetFastq attribute)
copy (wespipeline.utils.UncompressFile attribute)
cpus (wespipeline.align.FastqAlign attribute)
(wespipeline.processalign.AlignProcessing attribute)
(wespipeline.vcf.VariantCalling attribute)
create_gvcf (wespipeline.vcf.DeepvariantDockerTask attribute)
create_report (wespipeline.fastq.GetFastq attribute)
D
decomposes_multiallelic_variants (wespipeline.vcfanalysis.DockerVTnormalizeVCF attribute)
DeepvariantCallVariants (class in wespipeline.vcf)
DeepvariantDockerTask (class in wespipeline.vcf)
DockerGatkCallVariants (class in wespipeline.vcf)
DockerVTnormalizeVCF (class in wespipeline.vcfanalysis)
E
exp_name (wespipeline.utils.GlobalParams attribute)
F
FaidxIndex (class in wespipeline.reference)
fastq1_local_file (wespipeline.fastq.GetFastq attribute)
fastq1_url (wespipeline.fastq.GetFastq attribute)
fastq2_local_file (wespipeline.fastq.GetFastq attribute)
fastq2_url (wespipeline.fastq.GetFastq attribute)
fastq_file (wespipeline.fastq.FastqcQualityCheck attribute)
fastq_local_file (wespipeline.fastq.UncompressFastqgz attribute)
fastq_url (wespipeline.fastq.UncompressFastqgz attribute)
FastqAlign (class in wespipeline.align)
FastqcQualityCheck (class in wespipeline.fastq)
file (wespipeline.utils.LocalFile attribute)
FreebayesCallVariants (class in wespipeline.vcf)
from2bit (wespipeline.reference.GetReferenceFa attribute)
(wespipeline.reference.ReferenceGenome attribute)
G
GatkCallVariants (class in wespipeline.vcf)
GetFastq (class in wespipeline.fastq)
GetProgram (class in wespipeline.reference)
GetReferenceFa (class in wespipeline.reference)
GlobalParams (class in wespipeline.utils)
GunzipFile (class in wespipeline.utils)
I
image() (wespipeline.vcf.DeepvariantDockerTask property)
(wespipeline.vcf.DockerGatkCallVariants property)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF property)
IndexBam (class in wespipeline.processalign)
IndexNoDup (class in wespipeline.processalign)
input_file (wespipeline.utils.GunzipFile attribute)
(wespipeline.utils.UncompressFile attribute)
L
LocalFile (class in wespipeline.utils)
log_dir (wespipeline.utils.GlobalParams attribute)
M
MetaOutputHandler (class in wespipeline.utils)
model_type (wespipeline.vcf.DeepvariantDockerTask attribute)
(wespipeline.vcf.DockerGatkCallVariants attribute)
mount_tmp() (wespipeline.vcf.DeepvariantDockerTask property)
(wespipeline.vcf.DockerGatkCallVariants property)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF property)
N
name (in module wespipeline)
no_dup_bai_local_file (wespipeline.processalign.AlignProcessing attribute)
no_dup_bam_local_file (wespipeline.processalign.AlignProcessing attribute)
normalize (wespipeline.vcfanalysis.VariantCallingAnalysis attribute)
NormalizeVcfFiles (class in wespipeline.vcfanalysis)
O
out (wespipeline.vcfanalysis.VTnormalizeVCF attribute)
output() (wespipeline.align.BwaAlignFastq method)
(wespipeline.fastq.FastqcQualityCheck method)
(wespipeline.fastq.SraToolkitFastq method)
(wespipeline.fastq.UncompressFastqgz method)
(wespipeline.processalign.IndexBam method)
(wespipeline.processalign.IndexNoDup method)
(wespipeline.processalign.PicardMarkDuplicates method)
(wespipeline.processalign.SortSam method)
(wespipeline.reference.BwaIndex method)
(wespipeline.reference.FaidxIndex method)
(wespipeline.reference.GetProgram method)
(wespipeline.reference.PicardDict method)
(wespipeline.reference.TwoBitToFa method)
(wespipeline.utils.GunzipFile method)
(wespipeline.utils.LocalFile method)
(wespipeline.utils.MetaOutputHandler method)
(wespipeline.utils.UncompressFile method)
(wespipeline.utils.Wget method)
(wespipeline.vcf.DeepvariantCallVariants method)
(wespipeline.vcf.DeepvariantDockerTask method)
(wespipeline.vcf.DockerGatkCallVariants method)
(wespipeline.vcf.FreebayesCallVariants method)
(wespipeline.vcf.GatkCallVariants method)
(wespipeline.vcf.PlatypusCallVariants method)
(wespipeline.vcf.VarscanCallVariants method)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF method)
(wespipeline.vcfanalysis.NormalizeVcfFiles method)
(wespipeline.vcfanalysis.VTnormalizeVCF method)
(wespipeline.vcfanalysis.VariantCallingAnalysis method)
(wespipeline.vcfanalysis.VcftoolsCompare method)
(wespipeline.vcfanalysis.VcftoolsDepthAnalysis method)
(wespipeline.vcfanalysis.VcftoolsFreqAnalysis method)
output_file (wespipeline.fastq.UncompressFastqgz attribute)
(wespipeline.utils.UncompressFile attribute)
(wespipeline.utils.Wget attribute)
P
paired_end (wespipeline.fastq.GetFastq attribute)
(wespipeline.fastq.SraToolkitFastq attribute)
PicardDict (class in wespipeline.reference)
PicardMarkDuplicates (class in wespipeline.processalign)
PlatypusCallVariants (class in wespipeline.vcf)
program_args() (wespipeline.align.BwaAlignFastq method)
(wespipeline.fastq.FastqcQualityCheck method)
(wespipeline.fastq.SraToolkitFastq method)
(wespipeline.processalign.IndexBam method)
(wespipeline.processalign.IndexNoDup method)
(wespipeline.processalign.PicardMarkDuplicates method)
(wespipeline.processalign.SortSam method)
(wespipeline.reference.BwaIndex method)
(wespipeline.reference.FaidxIndex method)
(wespipeline.reference.GetProgram method)
(wespipeline.reference.PicardDict method)
(wespipeline.reference.TwoBitToFa method)
(wespipeline.utils.GunzipFile method)
(wespipeline.utils.UncompressFile method)
(wespipeline.utils.Wget method)
(wespipeline.vcf.DeepvariantCallVariants method)
(wespipeline.vcf.FreebayesCallVariants method)
(wespipeline.vcf.GatkCallVariants method)
(wespipeline.vcf.PlatypusCallVariants method)
(wespipeline.vcf.VarscanCallVariants method)
(wespipeline.vcfanalysis.VTnormalizeVCF method)
(wespipeline.vcfanalysis.VcftoolsCompare method)
(wespipeline.vcfanalysis.VcftoolsDepthAnalysis method)
(wespipeline.vcfanalysis.VcftoolsFreqAnalysis method)
R
ref_url (wespipeline.reference.GetReferenceFa attribute)
(wespipeline.reference.ReferenceGenome attribute)
(wespipeline.reference.TwoBitToFa attribute)
reference_local_file (wespipeline.reference.GetReferenceFa attribute)
(wespipeline.reference.ReferenceGenome attribute)
(wespipeline.reference.TwoBitToFa attribute)
ReferenceGenome (class in wespipeline.reference)
requires() (wespipeline.align.BwaAlignFastq method)
(wespipeline.align.FastqAlign method)
(wespipeline.fastq.GetFastq method)
(wespipeline.fastq.UncompressFastqgz method)
(wespipeline.processalign.AlignProcessing method)
(wespipeline.processalign.IndexBam method)
(wespipeline.processalign.IndexNoDup method)
(wespipeline.processalign.PicardMarkDuplicates method)
(wespipeline.processalign.SortSam method)
(wespipeline.reference.BwaIndex method)
(wespipeline.reference.FaidxIndex method)
(wespipeline.reference.GetProgram method)
(wespipeline.reference.GetReferenceFa method)
(wespipeline.reference.PicardDict method)
(wespipeline.reference.ReferenceGenome method)
(wespipeline.reference.TwoBitToFa method)
(wespipeline.utils.GunzipFile method)
(wespipeline.utils.UncompressFile method)
(wespipeline.utils.Wget method)
(wespipeline.vcf.DeepvariantCallVariants method)
(wespipeline.vcf.DeepvariantDockerTask method)
(wespipeline.vcf.DockerGatkCallVariants method)
(wespipeline.vcf.FreebayesCallVariants method)
(wespipeline.vcf.GatkCallVariants method)
(wespipeline.vcf.PlatypusCallVariants method)
(wespipeline.vcf.VariantCalling method)
(wespipeline.vcf.VarscanCallVariants method)
(wespipeline.vcfanalysis.DockerVTnormalizeVCF method)
(wespipeline.vcfanalysis.NormalizeVcfFiles method)
(wespipeline.vcfanalysis.VTnormalizeVCF method)
(wespipeline.vcfanalysis.VariantCallingAnalysis method)
(wespipeline.vcfanalysis.VcftoolsCompare method)
(wespipeline.vcfanalysis.VcftoolsDepthAnalysis method)
(wespipeline.vcfanalysis.VcftoolsFreqAnalysis method)
run() (wespipeline.align.FastqAlign method)
(wespipeline.fastq.GetFastq method)
(wespipeline.fastq.UncompressFastqgz method)
(wespipeline.processalign.AlignProcessing method)
(wespipeline.reference.ReferenceGenome method)
(wespipeline.utils.LocalFile method)
(wespipeline.vcf.VariantCalling method)
(wespipeline.vcfanalysis.NormalizeVcfFiles method)
(wespipeline.vcfanalysis.VariantCallingAnalysis method)
S
sam_local_file (wespipeline.align.FastqAlign attribute)
SortSam (class in wespipeline.processalign)
SraToolkitFastq (class in wespipeline.fastq)
T
TwoBitToFa (class in wespipeline.reference)
U
UncompressFastqgz (class in wespipeline.fastq)
UncompressFile (class in wespipeline.utils)
url (wespipeline.utils.Wget attribute)
use_deepvariant (wespipeline.vcf.VariantCalling attribute)
use_freebayes (wespipeline.vcf.VariantCalling attribute)
use_gatk (wespipeline.vcf.VariantCalling attribute)
use_platypus (wespipeline.vcf.VariantCalling attribute)
use_varscan (wespipeline.vcf.VariantCalling attribute)
V
VariantCalling (class in wespipeline.vcf)
VariantCallingAnalysis (class in wespipeline.vcfanalysis)
VarscanCallVariants (class in wespipeline.vcf)
vcf (wespipeline.vcfanalysis.DockerVTnormalizeVCF attribute)
(wespipeline.vcfanalysis.VTnormalizeVCF attribute)
(wespipeline.vcfanalysis.VcftoolsDepthAnalysis attribute)
(wespipeline.vcfanalysis.VcftoolsFreqAnalysis attribute)
vcf1 (wespipeline.vcfanalysis.VcftoolsCompare attribute)
vcf2 (wespipeline.vcfanalysis.VcftoolsCompare attribute)
vcf_local_files (wespipeline.vcf.VariantCalling attribute)
VcftoolsCompare (class in wespipeline.vcfanalysis)
VcftoolsDepthAnalysis (class in wespipeline.vcfanalysis)
VcftoolsFreqAnalysis (class in wespipeline.vcfanalysis)
VERSION (wespipeline.vcfanalysis.DockerVTnormalizeVCF attribute)
VTnormalizeVCF (class in wespipeline.vcfanalysis)
W
wespipeline (module)
wespipeline.align (module)
wespipeline.fastq (module)
wespipeline.processalign (module)
wespipeline.reference (module)
wespipeline.utils (module)
wespipeline.vcf (module)
wespipeline.vcfanalysis (module)
Wget (class in wespipeline.utils)
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