Using TASSEL GBS V2 pipeline to call SNPs with GBS raw data of 94 ponderosa pine (Pinus ponderosa) and the reference genome of loblolly pine (Pinus taeda).
- Version: TASSEL Version 5.0, GBS V2
- Website: http://www.maizegenetics.net/tassel
- Manual: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline
- Raw fasta file produced by GBS (Genotyping by sequencing) with restriction enzyme ApeKI
- Reference genome of loblolly pine (Pinus taeda)
- Barcode information
- Code: S1_fqtodb.sh
- Input: Two fasta file & one barcode file
- Plugin: -GBSSeqToTagDBPlugin
- Restriction enzyme: ApeKI
- Minimum Kmer length: 20
- Maximum Kmer length: 64
- Minimum Kmer count: 5
- Minimum count reads: 1
- Output: A .db file
- Code: S2_dbtotagfq.sh
- Input: .db file
- Plugin: -TagExportToFastqPlugin
- Minimum count reads: 1
- Output: .fa.gz file
- Code: S3_BWA_1.sh
- Input: reference fasta file
- Output: five files
- Code: S3_BWA_2.sh
- Input: .fa.gz file and the five files from Step 3_bwa_1
- Output: .sai file
- Code: S3_BWA_3.sh
- Input: .fa.gz file, the five files from Step 3_bwa_1, and the .sai file
- Output: .sam file
- Code: S3_bowtie2_1.sh
- Input: reference fasta file
- Output: five files and .fa.gz file
- Code: S3_bowtie2_2.sh
- Input: five files and .fa.gz file from step 3_bowtie2_1
- Output: .sam file
- Code: S4_samtodb.sh
- Input: .sam file from step bowtie2_2, .db file from step 2
- Plugin: -SAMToGBSdbPlugin
- Output: updated .db file
- Code: S5_discSNP.sh
- Input: updated .db file from Step 4
- Plugin: -DiscoverySNPCallerPluginV2
- -mnLCov : 0.1
- Output: updated .db file
- Code: S6_prodSNP_vcf.sh
- Input: raw fasta file, barcode file, updated .db file from Step 5
- Kmer length: 64
- Plugin: -ProductionSNPCallerPluginV2
- mnQS: 20
- Output: .vcf file
- Code: S6_prodSNP_h5.sh
- Input:raw fasta file, barcode file, updated .db file from Step 5
- Kmer length: 64
- Plugin: -ProductionSNPCallerPluginV2
- mnQS: 20
- Output: .h5 file