Difference between revisions of "SK met"

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(process)
(process)
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# samtools rmdup
 
# samtools rmdup
 
# /data/haggui$ /data/haggui/samtools-1.3.1/samtools mpileup -f Vradi_ver6.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b {bamfile.list}| bcftools call -v -m -O v > output
 
# /data/haggui$ /data/haggui/samtools-1.3.1/samtools mpileup -f Vradi_ver6.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b {bamfile.list}| bcftools call -v -m -O v > output
# vcftools --vcf SK_met_variant.vcf --minQ 30 --minDP 5 --maxDP 100 --recode --out SK_met_variant.vcf.SNP.q30.d5D100 --remove-indels (SK는 d3D20, K는 d5D100) = rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf  
+
# vcftools --vcf SK_met_variant.vcf --minQ 30 --minDP 5 --maxDP 100 --recode --out SK_met_variant.vcf.SNP.q30.d5D100 --remove-indels (SK는 d3D20, K는 d10D100) = rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf  
 
# homo and all genotype 있는 것만 골라내기 rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf.homo
 
# homo and all genotype 있는 것만 골라내기 rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf.homo
 
# -Xmx4g -jar /data2/chojam96/methylation/snpEff_program/snpEff/snpEff.jar -v Vradi_ensembl KJ.vcf > KJ.snpeff
 
# -Xmx4g -jar /data2/chojam96/methylation/snpEff_program/snpEff/snpEff.jar -v Vradi_ensembl KJ.vcf > KJ.snpeff

Revision as of 05:34, 14 March 2019

materials

raw_data : /NGS/NGS/VignaRadiata/DNA/SK/
/mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.reseqKJ.sorted.bam
SK010 TN1509D0657--TCCGGAGA-AGGCTATA
SK068 TN1509D0710--TAATGCGC-TAAGATTA
SK186 TN1510D0932--TCTCGCGC-TCAGAGCC
SK049 TN1509D0695--GAATTCGT-ACGTCCTG
SK094 TN1509D0736--TCTCGCGC-GTCAGTAC
SK152 TN1510D0898--CTGAAGCT-GCCTCTAT
SK176 TN1510D0922--TCCGCGAA-GCCTCTAT
SK156 TN1510D0902--CTGAAGCT-TAAGATTA
  • 244 > 63 /data/haggui/raw_data/ 에 sample#.fq.gz 로 저장함
ref : 244 /mount_test/sdd1/Mungbean_assemble/ver6/SNP/Vradi_ver6.fa 
  • 244 > 63 data/haggui/Vradi_ver6.fa

process

  1. java -jar jar /jungminh/~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 <input_forward.fq.gz> <input_reverse.fq.gz> <output_forward_paired.fq.gz> <output_forward_unpaired.fq.gz> <output_reverse_paired.fq.gz> <output_reverse_unpaired.fq.gz> ILLUMINACLIP:/jungminh/~/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
  2. bwa index <ref.fa>
  3. zcat unpaired_1 unpaired_2 | gzip '-c' > unpaired.fq.gz
  4. bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam" (1.5일)
  5. bwa mem Vradi_ver6.fa unpaired.fq.gz | samtools view -bS -q 30 -> unpaired.bam
  6. samtools sort
  7. samtools merge
  8. samtools depth {sorted.bam} > {.dep}
  9. wc -l *.dep
  10. cat {sort.bam.dep} |awk '{sum += $3} END { print sum}'
  11. samtools rmdup
  12. /data/haggui$ /data/haggui/samtools-1.3.1/samtools mpileup -f Vradi_ver6.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b {bamfile.list}| bcftools call -v -m -O v > output
  13. vcftools --vcf SK_met_variant.vcf --minQ 30 --minDP 5 --maxDP 100 --recode --out SK_met_variant.vcf.SNP.q30.d5D100 --remove-indels (SK는 d3D20, K는 d10D100) = rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf
  14. homo and all genotype 있는 것만 골라내기 rmdup.tr.combined.SK.variant.vcf.SNP.q30.d3D20.recode.vcf.homo
  15. -Xmx4g -jar /data2/chojam96/methylation/snpEff_program/snpEff/snpEff.jar -v Vradi_ensembl KJ.vcf > KJ.snpeff
  16. mergeskkjvcf.py > filteredSNP.combined
  17. temsnpindmr.py > snpindmr0311_2
  18. python combinemetlevel.py CpG_Vr-Met-S_bismark.cov.dmr.metlevel CpG_Vr-Met-SK010_bismark.cov.dmr.metlevel CpG_Vr-Met-SK049_bismark.cov.dmr.metlevel CpG_Vr-Met-SK068_bismark.cov.dmr.metlevel CpG_Vr-Met-SK094_bismark.cov.dmr.metlevel CpG_Vr-Met-SK152_bismark.cov.dmr.metlevel CpG_Vr-Met-SK156_bismark.cov.dmr.metlevel CpG_Vr-Met-SK176_bismark.cov.dmr.metlevel CpG_Vr-Met-SK186_bismark.cov.dmr.metlevel CpG_Vr-Met-K_bismark.cov.dmr.metlevel snpindmr0311_2 | sort > dmr.in.snp.over8

vcf를 193 으로 옮긴 후, snpeff 실행