Commit c3c219ab authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update !all_species_F_M_Wsnps.md

parent 4682416e
......@@ -253,3 +253,27 @@ LG6 114272754 . C T 999 . . GT NA NA 0 0 0 1 1 1 1 1 0 0 1 1 2 2 2 2 2 2 2 2
LG6 118233256 . G C 860 . . GT 0 0 0 0 0 0 0 0 1 1 NA 0 0 0 0 0 0 2 2 2 2 2
```
```
w_snps_coordinates.txt
sed 's/ /\t/g' w_snps_coordinates.txt > w_snps_coordinates.log
vcftools --vcf head.sin.kaz.urm_filtered.vcf --positions w_snps_coordinates.log --recode --recode-INFO-all --out w_snps.vcf
#doesn't work!
```
Maybe if i change filtering i fill find more sites
```
#filter for quality and coverage
srun vcftools --gzvcf head.sin.kaz.urm_vcf.gz --remove-indels --maf 0.1 --max-missing 0.9 --minQ 30 --min-meanDP 5 --max-meanDP 1000 --minDP 5 --maxDP 1000 --recode --stdout > head.sin.kaz.urm_diff_filtered.vcf
sbatch snp_calling_sin.kaz.urm_diff.sh
Submitted batch job 24850283
cat head.sin.kaz.urm_diff_filtered.vcf | grep -v '^##' | perl -pi -e 's/:.*?\t/\t/gi' | perl -pi -e 's/:.*//gi' | perl -pi -e 's/\t/ /gi' | perl -pi -e 's/0\/0/0/gi' | perl -pi -e 's/1\/1/2/gi' | perl -pi -e 's/0\/1/1/gi' | perl -pi -e 's/\.\/\./NA/gi' > head.sin.kaz.urm_diff_filtered.vcf_simple
grep -f w_snps_coordinates.txt head.sin.kaz.urm_diff_filtered.vcf_simple > w_snps_all_species_diff.txt
wc w_snps_all_species_diff.txt
47 1457 3557 w_snps_all_species_diff.txt
#more SNPs but still no signal :()
```
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