下載測(cè)試數(shù)據(jù)
cat list.txt | while read id ;do (prefetch ${id}) ;done
#list.txt的內(nèi)容是
SRR5943131
SRR5943132
SRR5943133
nohup ls *| while read id;do (fastq-dump --gzip --split-3 -O ./ ${id});done &
#sra中抽取fastq序列乡范，是逐個(gè)sra文件進(jìn)行的，不是同時(shí)多個(gè)sra文件一起運(yùn)行
ls *vcf.gz | while read id ;do (nohup bcftools call -m -v -o ${id%%.*}.call.vcf $id 2>${id%%.*}.log &) ;done
for i in *vcf ;do ( nohup bgzip -c $i > $i.gz &) ;done
for i in *call.vcf.gz ;do tabix -p vcf $i ;done
for i in *call.vcf.gz ;do
samtools faidx ../../AquilegiaOxysepala-v2.fasta chr03:21098978-21106544 | bcftools consensus $i > ${i%%.*}_C2H2.fasta ;done
for i in *_1.clean.fq.gz ;do (nohup bwa mem ../../AquilegiaOxysepala-v2.fasta
${i%_*}_1.clean.fq.gz ${i%_*}_2.clean.fq.gz > ${i%%_*}.sam 2> ${i%%_*}.log &)
;done
samtools view -b BJ0101.sam > BJ0101.bam
samtools sort -m 100000000000 -o BJ0101.sort.bam BJ0101.bam
samtools rmdup -S BJ0101.sort.bam BJ0101.sort.rmdup.bam
samtools mpileup -C 50 -q 25 -f AquilegiaOxysepala-v2.fasta --output
BJ0101.vcf -v -u -t DP -t AD -t SP -e -h -L -o -p BJ0101.sort.rmdup.bam
