Source data - HackMD

# Source data ## SRA list ``` merged_SRR351213 merged_SRR351222 merged_SRR351225 merged_SRR998947 merged_SRR998948 merged_SRR998949 merged_SRR998950 merged_SRR998951 merged_SRR998952 merged_SRR998953 merged_SRR998954 merged_SRR998956 merged_SRR998957 merged_SRR998958 merged_SRR998959 merged_SRR998960 merged_SRR998961 merged_SRR998962 merged_SRR998963 merged_SRR998964 merged_SRR998965 merged_SRR998966 merged_SRR998967 merged_SRR998968 merged_SRR998969 merged_SRR998973 merged_SRR998974 merged_SRR998975 merged_SRR998976 merged_SRR998977 merged_SRR998978 merged_SRR998979 merged_SRR998980 merged_SRR998981 merged_SRR998982 merged_SRR998983 merged_SRR999001 SRR5271054 SRR5271055 SRR5271056 SRR5271057 SRR5271058 SRR5271059 SRR5271061 SRR998970 SRR998971 SRR998972 SRR998984 SRR998985 SRR999016 SRR999017 SRR999028 SRR999030 SRR999031 ``` ## Reference genome version ``` Sbicolor_454_v3.0.1 ``` ##SRA downloader ``` fastq-dump --split-3 --gzip --qual-filter-1 ``` # Population structure ## BWA ### Version ``` bwa-0.7.17 ``` ## GATK ### Version ``` gatk-4.0.5.1 ``` ### options CreateSequenceDictionary IndexFeatureFile HaplotypeCaller CombineGVCFs MergeVcfs ## htslib ### Version ``` 1.8 ``` ## subtools ``` tabix ``` ## PLINK ### Version ``` 1.9 ``` ### options ``` --mind 0.7 --maf 0.05 --geno 0.01 --allow-extra-chr --indep-pairwise 50 10 0.1 --double-id --vcf-idspace-to "_" # removing individuals with genotyping error >5% and SNPs with maf <1% and genotype data <70% ``` ## Samtools ### Version ``` samtools v1.9 ``` ## Admixture ### Version ``` admixture_linux-1.3.0 ``` ## fastaStructure ### Version ``` fastStructure-e47212f ``` ### options (logistic) ``` --full --seed=100 --prior=logistic ``` # STR or SSR ## HipSTR Short tandem repeats ### option ``` --min-reads 25 --no-rmdup --max-mate-dist 1000 --max-str-len 500 --max-reads 200 --def-stutter-model --require-pairs ```