Commit 5dc0d4ec authored by Marwan ELKREWI's avatar Marwan ELKREWI
Browse files


parent bea23deb
......@@ -53,3 +53,17 @@ srun vcftools --gzvcf head_asex_raremale.vcf.gz --remove-indels --maf 0.1 --max-
#filter 2:remove multiallelic
bcftools view --max-alleles 2 --exclude-types indels head_asex_raremale_cov5_filtered.vcf > head_asex_raremale_cov5_filtered2.vcf
We then clean the vcf file by removing the extra information on top:
grep -v "##" head_asex_raremale_cov5_filtered2.vcf > head_asex_raremale_cov5_filtered2_clean_kaz_genome.vcf
To identify the heterozygous SNPs, we use the following python commands:
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import scipy
import os
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