Sep 25 2015 Indel analysis workflow (final)


StepAnnotation
Step 1: Input dataset
select at runtime
indexed Bam file
Step 2: Input dataset
select at runtime
Bed file contains the chromosomal positions to be used for alignment with Bam file as are reference to call for indels.
Step 3: MPileup
Use a built-in genome
BAM files
BAM file 1
Output dataset 'output' from step 1
mm10
Perform genotype likelihood computation (--VCF, --BCF options)
VCF
False
Nothing selected.
Perform INDEL calling and set advanced options
40
20
100
1000000
1
40
0.002
False
Platform for INDEL candidates
Advanced
Do not filter
From an uploaded BED file (--positions)
Output dataset 'output' from step 2
Do not exclude
False
False
False
0
250
False
0
13
Empty.
Step 4: VCFfilter:
Output dataset 'output_mpileup' from step 3
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'.