进到align目录
对质量好的测序数据进行比对

1. 一个个比对，生成BAM文件

align目录

sample=SRR7696207
bwa mem -t 2 -R "@RG\tID:$sample\tSM:$sample\tLB:WGS\tPL:Illumina" ../hg38/bwa_index/gatk_hg38 ../clean/SRR7696207_1_val_1.fq.gz ../clean/SRR7696207_2_val_2.fq.gz |samtools sort -@ 2 -o SRR7696207.bam -

不用-R参数也可以执行，但后面gatk的时候会报错

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 143150 sequences (20000163 bp)...
[M::process] read 142658 sequences (20000278 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 61056, 1, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (135, 165, 207)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 351)
[M::mem_pestat] mean and std.dev: (174.05, 52.67)
......

2或者循环批量比对

#clean目录
ls *1.fastq.gz > 1
ls *2.fastq.gz > 2
paste 1 2 > config
vim config

增加第一列文件名，记得不能空格，要Tab分隔
如果样本量很多就用脚本，具体见大样本分析那篇
align目录下

INDEX=../hg38/bwa_index/gatk_hg38
cat ../clean/config|while read id
do 
arr=($id)
sample=${arr[0]}
fq1=${arr[1]}
fq2=${arr[2]}
bwa mem -t 5 -R "@RG\tID:$sample\tSM:$sample\tLB:WGS\tPL:Illumina" $INDEX ../clean/$fq1 ../clean/$fq2 |samtools sort  -@ 2 -o $sample.bam -
done &

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 142876 sequences (20000122 bp)...
[M::process] read 142628 sequences (20000141 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 61992, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (137, 174, 219)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[M::mem_pestat] mean and std.dev: (181.21, 59.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 465)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 142876 reads in 24.094 CPU sec, 11.833 real sec

3 查看bam文件

$ samtools view -H SRR8517853.bam |grep -v "SQ"

@HD     VN:1.6  SO:coordinate
@RG     ID:SRR8517853/tSM:SRR8517853    LB:WGS  PL:Illumina
@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -t 2 -R @RG\tID:SRR8517853/tSM:SRR8517853\tLB:WGS\tPL:Illumina ../hg38/bwa_index/gatk_hg38 ../clean/SRR8517853_1_val_1.fq.gz ../clean/SRR8517853_2_val_2.fq.gz