Duplex Analysis from Aligned Families


StepAnnotation
Step 1: Input dataset
select at runtime
This should be the output of Du Novo's "Align families" tool
Step 2: Du Novo: Make consensus reads
Output dataset 'output' from step 1
3
20
Sanger (PHRED 0 = "!")
True
Step 3: Sequence Content Trimmer
Paired
Output dataset 'output1' from step 2
Output dataset 'output2' from step 2
NRYSWKMBDHV
0.2
10
False
True
50
Step 4: Sequence Content Trimmer
Unpaired
Output dataset 'sscs' from step 2
NRYSWKMBDHV
0.2
10
False
True
50
Step 5: Combine FASTA and QUAL
Output dataset 'output1' from step 3
select at runtime
ASCII
Step 6: Combine FASTA and QUAL
Output dataset 'output2' from step 3
select at runtime
ASCII
Step 7: Combine FASTA and QUAL
Output dataset 'output1' from step 4
select at runtime
ASCII
Step 8: Map with BWA-MEM
Use a built-in genome index
hg38
Paired
Output dataset 'output_file' from step 5
Output dataset 'output_file' from step 6
Empty.
Set read groups (SAM/BAM specification)
False
bwa-mem
False
bwa-mem
ILLUMINA
False
abl1
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 9: Map with BWA
Use a built-in genome index
hg38
Paired fastq
Output dataset 'output_file' from step 5
Output dataset 'output_file' from step 6
Do not set
Set read groups (SAM/BAM specification)
False
bwa
False
bwa
ILLUMINA
False
abl1
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 10: Map with BWA-MEM
Use a built-in genome index
hg38
Single
Output dataset 'output_file' from step 7
Set read groups (SAM/BAM specification)
False
bwa-mem_SSCS
False
bwa-mem_SSCS
ILLUMINA
False
abl1
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 11: Map with BWA
Use a built-in genome index
hg38
Single fastq
Output dataset 'output_file' from step 7
Do not set
Set read groups (SAM/BAM specification)
False
bwa_SSCS
False
bwa_SSCS
ILLUMINA
False
abl1
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 12: MergeSamFiles
Output dataset 'bam_output' from step 8,Output dataset 'bam_output' from step 9
False
False
Comments
Lenient
Step 13: MergeSamFiles
Output dataset 'bam_output' from step 10,Output dataset 'bam_output' from step 11
False
False
Comments
Lenient
Step 14: Naive Variant Caller
Locally cached
BAM files
BAM file 1
Output dataset 'outFile' from step 12
hg38
Restrict to regions
Restrict to regions 1
Not available.
Not available.
Not available.
0
20
20
1
False
True
Hide Advanced Options
Step 15: Naive Variant Caller
Locally cached
BAM files
BAM file 1
Output dataset 'outFile' from step 13
hg38
Restrict to regions
Restrict to regions 1
Not available.
Not available.
Not available.
0
20
20
1
False
True
Hide Advanced Options
Step 16: Variant Annotator
Output dataset 'output_vcf' from step 14
1.0
10
False
True
True
Empty.
Step 17: Variant Annotator
Output dataset 'output_vcf' from step 15
1.0
10
False
True
True
Empty.
Step 18: Filter
Output dataset 'output' from step 16
c16 >= 0.01
1
Column 16 contains minor allele frequencies (MAF). Here we filter only sites where the MAF >= 0.01 (or 1%)
Step 19: Filter
Output dataset 'output' from step 17
c16 >= 0.01
0
Column 16 contains minor allele frequencies (MAF). Here we filter only sites where the MAF >= 0.01 (or 1%)