Commit b374613e authored by Marwan ELKREWI's avatar Marwan ELKREWI
Browse files

Update Heterozygosity_rare_male.md

parent b54d3654
......@@ -49,7 +49,7 @@ srun bcftools mpileup -a AD,DP,SP -Ou --threads 40 -f k41_scaffolds_kazakh_male_
#filter for quality and coverage
srun vcftools --gzvcf head_asex_raremale.vcf.gz --remove-indels --maf 0.1 --max-missing 0.9 --minQ 30 --min-meanDP 5 --max-meanDP 100 --minDP 5 --maxDP 100 --recode --stdout > head_asex_raremale_cov5_filtered.vcf
```
#filter2:remove multiallelic
bcftools view --max-alleles 2 --exclude-types indels head_asex_raremale_cov5_filtered.vcf > head_asex_raremale_cov5_filtered2.vcf
```
......
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