Identify and Validate Coding Variants from Exome Sequencing Data

Annotation: Identify and Validate Coding Variants from Exome Sequencing Data

StepAnnotation
Step 1: Input dataset
select at runtime
Aligned Reads (e.g., HG00096.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 2: Input dataset
select at runtime
Aligned Reads (e.g., HG00097.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 3: Input dataset
select at runtime
Aligned Reads (e.g., HG00099.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 4: Input dataset
select at runtime
Aligned Reads (e.g., HG00100.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 5: Input dataset
select at runtime
Aligned Reads (e.g., HG00101.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 6: Input dataset
select at runtime
Aligned Reads (e.g., HG00107.chrom20.ILLUMINA.bwa.GBR.exome.20120522.bam)
Step 7: Input dataset
select at runtime
Aligned Reads (e.g., HG00103.chrom20.ILLUMINA.bwa.GBR.exome.20120522.bam)
Step 8: Input dataset
select at runtime
Aligned Reads (e.g., HG00102.chrom20.ILLUMINA.bwa.GBR.exome.20121211.bam)
Step 9: Input dataset
select at runtime
Aligned Reads (e.g., HG00105.chrom20.ILLUMINA.bwa.GBR.exome.20120522.bam)
Step 10: Input dataset
select at runtime
Aligned Reads (e.g., HG00106.chrom20.ILLUMINA.bwa.GBR.exome.20120522.bam)
Step 11: Input dataset
select at runtime
hs_ref_GRCh37.p5_chr20.fa
Step 12: Input dataset
select at runtime
hapmap_3.3.b37.chr20.vcf
Step 13: FreeBayes
History
Sample BAM files
Sample BAM file 1
Output dataset 'output' from step 1
Sample BAM file 2
Output dataset 'output' from step 2
Sample BAM file 3
Output dataset 'output' from step 3
Sample BAM file 4
Output dataset 'output' from step 4
Sample BAM file 5
Output dataset 'output' from step 5
Sample BAM file 6
Output dataset 'output' from step 8
Sample BAM file 7
Output dataset 'output' from step 7
Sample BAM file 8
Output dataset 'output' from step 9
Sample BAM file 9
Output dataset 'output' from step 10
Sample BAM file 10
Output dataset 'output' from step 6
Output dataset 'output' from step 11
Do not limit
1:Simple diploid calling
Use default job resource parameters
Step 14: VCFfilter:
Output dataset 'output_vcf' from step 13
more filters
False

No value found for 'Filter entire records, not just alleles'. Using default: 'False'.

False

No value found for 'Tag vcf records as positively filtered with this tag, print all records'. Using default: 'False'.

False

No value found for 'Tag vcf records as negatively filtered with this tag, print all records'. Using default: 'False'.

False

No value found for 'Append the existing filter tag, don't just replace it'. Using default: 'False'.

False

No value found for 'Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag'. Using default: 'False'.

False

No value found for 'Inverts the filter, e.g. grep -v'. Using default: 'False'.

False

No value found for 'Use logical OR instead of AND to combine filters'. Using default: 'False'.

Not available.

No value found for 'Specify a region on which to target the filtering'.

Step 15: VCF-VCFintersect:
Output dataset 'output' from step 12
Output dataset 'out_file1' from step 14
History
Output dataset 'output' from step 11
Intersect
False
30
False
Don't use advanced options
Step 16: Unknown Tool with id 'genomespace_exporter'