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
/galaxy/data/hg19/bwa_index/hg19.fa
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
Locally cached
Output dataset 'output' from step 3
Step 5: Mark Duplicate reads
Output dataset 'output1' from step 4
${sample_name}: mapped reads, no dups
True
True
[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*
100
Step 6: flagstat
Output dataset 'output1' from step 4
Step 7: MPileup
Locally cached
BAM files
BAM file 1
Output dataset 'out_file' from step 5
hg19
Do not perform genotype likelihood computation
Basic
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