---
# System prepended metadata

title: Source data

---

# 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
```

