Difference between revisions of "SK met"
From Crop Genomics Lab.
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# bwa index <ref.fa> | # bwa index <ref.fa> | ||
# cat SK_met.list | parallel --gnu -j 3 "bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam" | # cat SK_met.list | parallel --gnu -j 3 "bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam" | ||
| + | # samtools sort/index/ bam samtools faidx ref | ||
| + | # /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 > SK_met_variant.vcf | ||
| + | |||
| + | 버전 안맞아서 samtools-1.3 써야함 | ||
Revision as of 02:09, 25 January 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
- bwa index <ref.fa>
- cat SK_met.list | parallel --gnu -j 3 "bwa mem Vradi_ver6.fa ./raw_data/{}_1.fq.gz ./raw_data/{}_2.fq.gz | samtools view -bS -q 30 -> {}.bam"
- samtools sort/index/ bam samtools faidx ref
- /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 > SK_met_variant.vcf
버전 안맞아서 samtools-1.3 써야함
