UNEAK

Using UNEAK (de novo) pipelineto call SNPs with GBS raw data of 94 ponderosa pine (Pinus ponderosa)

Software

Version: TASSEL Version 3.0, UNEAK
Website: https://tassel.bitbucket.io/TasselArchived.html
Manual: https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/TasselPipelineUNEAK.pdf

Input File

Raw fasta file produced by GBS (Genotyping by sequencing) with restriction enzyme ApeKI
Barcode information

Output File

Step 1: create working directory

Code: S1_crtDir.sh
Plugin: -UCreatWorkingDirPlugin
Output: Eight folders

Step 2: fastq to tag count

Code: S2_fqtotag.sh
Input: barcode file and the raw fasta file
Plugin: -UFastqToTagCountPlugin
Output: 96 tag counts .cnt file

Step 3: merge tag count

Code: S3_mergetag.sh
Input: 96 tag counts .cnt file
Plugin: -UMergeTaxaTagCountPlugin
Minimum count reads: 1
Output: 1 merged all tag counts .cnt file

Step 4: merged tag count to tag pairs

Code: S4_tagctotagp.sh
Input: 1 merged all tag counts .cnt file
Plugin: -UTagCountToTagPairPlugin
QS: 0.01
Output: 1 tag pair .tps file

Step 5: tag pairs to tbt

Code: S5_tagptotbt.sh
Input: 1 tag pair .tps file, 96 tag counts .cnt file from step 2
Plugin: -UTagPairToTBTPlugin
Output: a tag by taxa .bin file

Step 6: tbt to map info

Code: S6_tbttomapinf.sh
Input: 1 tag pair .tps file from step 4, a tag by taxa .bin file from step 5
Plugin: -UTBTToMapInfoPlugin
Output: a map information .bin file

Step 7: map info to hapmap

Code: S7_mapinftohm.sh
Input: a map information .bin file
mnMAF: 0.01
minimum count reads: 1
minimum call rate: 0.1
maximum call rate: 1
Plugin: -UMapInfoToHapMapPlugin
Output: a .hmp file, a .hmc file, a .fas file

Step 8: change hapmap file to vcf file

Code: hmptovcf_denovo.sh
Input: a .hmp file
Output: a .vcf file • hmptovcf_denovo.out