Exome Analysis

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Map with BWA for Illumina
Use a built-in index
Araly1
Paired-end
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Commonly Used
False
Use default job resource parameters
Step 4: SAM-to-BAM
Use a built-in genome
Output dataset 'output' from step 3
None
Use default job resource parameters
Step 5: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0'
Step 6: flagstat
Output dataset 'output1' from step 4
Step 7: samtools mpileup
Use a built-in genome
select at runtime
hg19
Basic
Default
Step 8: Varscan
Output dataset 'output_mpileup' from step 7
consensus genotype
8
2
15
0.01
0.75
0.99
no
${sample_name}
Step 9: Annotate
Output dataset 'output' from step 8
FORMAT/FREQ
MinAF [${allele_freq}]
MinAF
>= ${allele_freq}
Step 10: Filter
Output dataset 'output' from step 9
c7 == 'PASS'
26
Step 11: ANNOVAR Annotate VCF
Output dataset 'out_file1' from step 10
gencodeV19
None
1000g2012apr_all avsift esp6500si_all snp137 cosmic67