Difference between revisions of "Re-sequencing"
From Crop Genomics Lab.
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'''bwa pipe''' | '''bwa pipe''' | ||
+ | 'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3] | ||
'''bowtie2 pipe''' | '''bowtie2 pipe''' | ||
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4. sort bam | 4. sort bam | ||
+ | |||
5. bam index, fasta index | 5. bam index, fasta index | ||
− | 6. mpileup - | + | |
+ | 6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg - | ||
+ | |||
+ | <changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf> | ||
+ | |||
+ | |||
+ | Insert size estimation | ||
+ | |||
+ | samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size | ||
+ | |||
+ | get median or get mode | ||
+ | |||
+ | == Resequencing pipeline ppt == | ||
+ | [[File:Resequencing pipeline.pptx|thumbnail]] | ||
+ | |||
+ | [[File:Information processing after resequencing.pptx|thumbnail]] |
Latest revision as of 04:12, 3 July 2018
bwa pipe
'bwa mem /data1/ref/Gmax_275_v2.0.fa '+sys.argv[1]+' '+sys.argv[2]+'| samtools view -bS - > '+sys.argv[3]
bowtie2 pipe
1. Make bowtie index
bowtie2-build reference.fa reference.fa |
2. Align
bowtie2-align -p num_threads -x reference_index -1 paired_1 -2 paired_2 -S sam_output |
3. convert sam to bam
samtools view -Sb <SAMFILE> > <BAMFILE> |
variation discovery
4. sort bam
5. bam index, fasta index
6. samtools mpileup -DSug <bam1> <bam2> .... -f reference.fa(fasta indexed) | bcftools view -vcg -
<changed version, samtools mpileup -f scaffolds.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u -b bam_list | bcftools call -v -m -O v > variant.vcf>
Insert size estimation
samtools view /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam | awk '{if ($9 > 0) {print $9}}' > /alima9002/denovo/with_Gmax_275/CS-12/CS-12_Gmax_275.bam.sorted.bam.insert.size
get median or get mode