WES全外显子分析-生信技能树

下载测试数据

cat list.txt | while read id ;do (prefetch ${id}) ;done
#list.txt的内容是
SRR5943131
SRR5943132
SRR5943133

nohup ls *| while read id;do (fastq-dump --gzip --split-3 -O ./ ${id});done & 
#sra中抽取fastq序列，是逐个sra文件进行的，不是同时多个sra文件一起运行

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