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Revision as of 11:51, 23 October 2014
, 11:51, 23 October 2014→Required Files
=== Human Reference Files ===
=== Human Reference Files ===
Reference Sequence in fasta format
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Default Value
|-
| REF || $(REF_DIR)/human.g1k.v37.fa
|}
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Pipeline !! Use
|-
| align || mapping to reference, recalibration, quality control
|-
| snpcall || pileup & identify variants, summarize filtered variants
|-
| indel || discovery, genotyping
|}
All pipelines require additional files:
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Step !! Required Extensions !! Command to Create
|-
|all || -bs.umfa || automatically created in same directory as REF file by GotCloud
|}
The alignment pipeline requires additional files:
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Step !! Required Extensions !! Command to Create
| bwa mapping || .amb, .ann, .bwt, .pac, .sa || bin/bwa index ref.fa
|-
| qplot || .fa.GCcontent
|}
=== DBSNP VCF File ===
=== DBSNP VCF File ===
=== ===
=== HapMap3 Polymorphic Sites VCF File ===
=== INDEL VCF File(s) ===
=== OMNI VCF File ===
= Downloadable Reference and Resource Files =
= Downloadable Reference and Resource Files =
