SK met

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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
  1. bwa index <ref.fa>
  2. 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"
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