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

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