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

Update Heterozygosity_rare_male.md

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
```
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment