Commit 81ef4149 authored by Marwan ELKREWI's avatar Marwan ELKREWI
Browse files

Update Heterozygosity_rare_male.md

parent 4208e0fb
......@@ -26,13 +26,13 @@ srun java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/T
working directory: `/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/`
```
module load star/2.6.0c
module load star
STAR --runMode genomeGenerate --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --genomeFastaFiles /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/CHRR_integrated.fa --runThreadN 10 --genomeChrBinNbits 15
STAR --runMode genomeGenerate --genomeDir index --genomeFastaFiles k41_scaffolds_kazakh_male_genome_16_09_2021.scafSeq --runThreadN 40 --genomeChrBinNbits 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn asexualsister_Aibi_1_trimmed.fq asexualsister_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/asexualsister_Aibi_ --runThreadN 10
STAR --genomeDir ./index --readFilesIn raremale_Aibi_1_trimmed.fq raremale_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix raremale_Aibi_ --runThreadN 40
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn raremale_Aibi_1_trimmed.fq raremale_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/raremale_Aibi_ --runThreadN 10
STAR --genomeDir ./index --readFilesIn asexualsister_Aibi_1_trimmed.fq asexualsister_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix asexsister_Aibi_ --runThreadN 40
```
## 4. SNP calling and VCF creation.
......@@ -40,15 +40,17 @@ STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/
with the less strict filtering for coverage (>5,<100).
```
cd /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/
module load samtools
module load bcftools
module load vcftools
#Call SNPs from the BAM alignments
srun bcftools mpileup -a AD,DP,SP -Ou -f CHRR_integrated.fa asexualsister_Aibi_Aligned.sortedByCoord.out.bam raremale_Aibi_Aligned.sortedByCoord.out.bam | bcftools call -v -f GQ,GP -mO z -o head_asex_raremale.vcf.gz
srun bcftools mpileup -a AD,DP,SP -Ou --threads 40 -f k41_scaffolds_kazakh_male_genome_16_09_2021.scafSeq asexsister_Aibi_Aligned.sortedByCoord.out.bam raremale_Aibi_Aligned.sortedByCoord.out.bam | bcftools call -v -f GQ,GP -mO z -o head_asex_raremale.vcf.gz
#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
#filter 2: remove multiallelic
#filter 2:remove multiallelic
bcftools view --max-alleles 2 --exclude-types indels head_asex_raremale_cov5_filtered.vcf > head_asex_raremale_cov5_filtered2.vcf
```
......
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