Difference between revisions of "SK met"
From Crop Genomics Lab.
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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 | + | # 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 |
+ | # 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 | ||
vcf를 193 으로 옮긴 후, snpeff 실행 | vcf를 193 으로 옮긴 후, snpeff 실행 |
Revision as of 05:10, 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
- 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
- bwa index <ref.fa>
- zcat unpaired_1 unpaired_2 | gzip '-c' > unpaired.fq.gz
- bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam" (1.5일)
- bwa mem Vradi_ver6.fa unpaired.fq.gz | samtools view -bS -q 30 -> unpaired.bam
- samtools sort
- samtools merge
- samtools depth {sorted.bam} > {.dep}
- wc -l *.dep
- cat {sort.bam.dep} |awk '{sum += $3} END { print sum}'
- samtools rmdup
- /data/haggui$ /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
- 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
- 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
vcf를 193 으로 옮긴 후, snpeff 실행