Difference between revisions of "2021 sewon labnote"
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bwa mem -t 20 /data/ref/Gmax/assembly/Gmax_275_v2.0.fa ./jinpung_forward_paired.fastq.gz ./jingpung_reverse_paired.fastq.gz | samtools view -bS -q 30 -> jinpung.bam | bwa mem -t 20 /data/ref/Gmax/assembly/Gmax_275_v2.0.fa ./jinpung_forward_paired.fastq.gz ./jingpung_reverse_paired.fastq.gz | samtools view -bS -q 30 -> jinpung.bam | ||
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samtools sort ./jinpung.bam -o jinpung.sort.bam | samtools sort ./jinpung.bam -o jinpung.sort.bam | ||
Revision as of 06:03, 17 March 2021
Jingpung resequencing - trimmomatic result
java -jar /data/Program/Trimmomatic-0.39/trimmomatic-0.39.jar PE -phred33 jinpung_1.fastq.gz jinpung_2.fastq.gz output_forward_paired.fastq.gz output_forward_unpaired.fastq.gz output_reverse_paired.fastq.gz output_reverse_unpaired.fastq.gz ILLUMINACLIP:/data/Program/Trimmomatic-0.39/adapters/TruSeq3-PE.fa :2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
TrimmomaticPE: Started with arguments:
-phred33 jinpung_1.fastq.gz jinpung_2.fastq.gz output_forward_paired.fastq.gz output_forward_unpaired.fastq.gz output_reverse_paired.fastq.gz output_reverse_unpaired.fastq.gz ILLUMINACLIP:/data/Program/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences ll Input Read Pairs: 42918512 Both Surviving: 40100414 (93.43%) Forward Only Surviving: 2273317 (5.30%) Reverse Only Surviving: 297601 (0.69%) Dropped: 247180 (0.58%) TrimmomaticPE: Completed successfully
Jingpung making .bam file (w/ 20threads & q 30)
bwa mem -t 20 /data/ref/Gmax/assembly/Gmax_275_v2.0.fa ./jinpung_forward_paired.fastq.gz ./jingpung_reverse_paired.fastq.gz | samtools view -bS -q 30 -> jinpung.bam
bamfile edit:
samtools sort ./jinpung.bam -o jinpung.sort.bam
samtools index jinpung.sort.bam
samtools mpileup -f /data/ref/Gmax/assembly/Gmax_275_v2.0.fa -v -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -u jinpung.sort.bam | bcftools call -v -m -O v > jinpung.variant.vcf
[warning] samtools mpileup option `v` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[warning] samtools mpileup option `t` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future.
