bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
```
when all steps are finished: finish the terminal output log
```
exit
```
The final step consists of removing individuals with (extreme) outlier heterozygosity values. Here we define outliers as falling outside 6 * interquartile range.
This theshold value is set in accordance to our data and it is advised to look at the outputted figures to validate this choice for your data.
### SNP filtering results for Mullus surmuletus
| filtering step | filter for | individuals retained | SNPs retained | run time (sec) | output |