shumengjun / UNEAK

Calling SNPs using UNEAK (de novo) pipeline for ponderosa pine

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

VCF 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