Variant discovery and reference correction from separate reads
Created: 2013-05-14 01:40:34
Last updated: 2013-05-14 01:41:54
Error identification and error correction of reference genome assembly from deep-seq Illumina reads.
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Workflow Components
Inputs (5)
Name |
Description |
Lib 1 Left |
|
Lib 1 Right |
|
Lib 2 Left |
|
Lib 2 Right |
|
Reference Genome |
|
Steps (13)
Name |
Tool |
Description |
Input dataset |
None |
|
Input dataset |
None |
|
Unified Genotyper |
gatk_unified_genotyper |
|
Variant Filtration |
gatk_variant_filtration |
|
Generates an alternative reference sequence over the specified interval. |
gatk_fasta_alternate_reference_walker |
|
Input dataset |
None |
|
Input dataset |
None |
|
Input dataset |
None |
|
Map with BWA for Illumina |
bwa_wrapper |
|
Map with BWA for Illumina |
bwa_wrapper |
|
Merge BAM Files |
sam_merge2 |
|
Realigner Target Creator |
gatk_realigner_target_creator |
|
Indel Realigner |
gatk_indel_realigner |
|
Outputs (15)
Name |
Type |
output_vcf |
vcf |
output_metrics |
txt |
output_log |
txt |
output_vcf |
vcf |
output_log |
txt |
output_sequence |
fasta |
output_log |
txt |
output |
sam |
output |
sam |
output1 |
bam |
outlog |
txt |
output_interval |
gatk_interval |
output_log |
txt |
output_bam |
bam |
output_log |
txt |
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