Stacks_ref

Using Stacks pipeline to call SNPs with GBS raw data of 94 ponderosa pine (Pinus ponderosa) and the reference genome of loblolly pine (Pinus taeda).

Software:

• Version: Stacks Version 2.2
• Website: http://catchenlab.life.illinois.edu/stacks/
• Manual: http://catchenlab.life.illinois.edu/stacks/manual/

Input File

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

Output File

VCF file

Step1: clean the data

• Code: S1_radtags_05.sh, S1_radtags_06.sh
• Input: two raw fasta filet, barcode file
• sliding window: 0.2
• score limit: 20
• maximum read length: 64
• Output: 96 .fq.gz file

Step8: bwa

• Code: S8_bwa.sh
• Input: reference genome of loblolly pine, and output file of Step 1
• Output: 96 .sam file

Step9: sam to bam

• Code: S9_samtobam_05.sh, S9_samtobam_06.sh
• Input: output file of Step 8
• Output: 96 .bam file

Step10: sort bam files

• Code: S10_bamsorted_05.sh, S10_bamsorted_06.sh
• Input: output file of step 9
• Output: 96 sorted .bam file

Step11: gstacks_ref

• Code: S11_gstacks_ref.sh
• Input: output file of Step 10
• Output: one catalog .alleles.tsv.gz file, one catalog .tags.tsv.gz file, one catalog .snp.tsv.gz file

Step12: populations_ref

• Code: S12_populations_ref.sh
• Input: output file of Step 11
• Output: VCF file