BRCA1基因为例

1 找到BRCA1在gtf文件中的坐标

$ zcat  /mnt/f/kelly/bioTree/server/wesproject/reference/gencode.v25.annotation.gtf.gz |grep -w BRCA1|head|less -SN

     1 chr17   HAVANA  gene    43044295        43170245        .       -       .       gene_id "ENSG00000012048.20";
      2 chr17   HAVANA  transcript      43044295        43125370        .       -       .       gene_id "ENSG00000012
      3 chr17   HAVANA  exon    43125271        43125370        .       -       .       gene_id "ENSG00000012048.20";
      4 chr17   HAVANA  exon    43124017        43124115        .       -       .       gene_id "ENSG00000012048.20";
      5 chr17   HAVANA  CDS     43124017        43124096        .       -       0       gene_id "ENSG00000012048.20";
      6 chr17   HAVANA  start_codon     43124094        43124096        .       -       0       gene_id "ENSG00000012
      7 chr17   HAVANA  exon    43115726        43115779        .       -       .       gene_id "ENSG00000012048.20";
      8 chr17   HAVANA  CDS     43115726        43115779        .       -       1       gene_id "ENSG00000012048.20";
      9 chr17   HAVANA  exon    43106456        43106533        .       -       .       gene_id "ENSG00000012048.20";
     10 chr17   HAVANA  CDS     43106456        43106533        .       -       1       gene_id "ENSG00000012048.20";
~

2提取BRCA在各个bam文件的read信息

$ ls -lh SRR7696207*.bam|cut -d " " -f 5-

3.9G Jun  2 21:40 SRR7696207.bam
8.2G Jun  5 18:56 SRR7696207_bqsr.bam
5.1G Jun  2 22:06 SRR7696207_marked.bam
5.1G Jun  2 23:24 SRR7696207_marked_fixed.bam

提取上述个bam中的BRCA1基因的reads

samtools view -h SRR8517856.bam chr17:43044295-43170245|samtools sort -o SRR7696207.brca1.bam -
samtools view -h SRR8517856_bqsr.bam chr17:43044295-43170245|samtools sort -o SRR7696207_bqsr.brca1.bam -
samtools view -h SRR8517856_marked.bam chr17:43044295-43170245|samtools sort -o SRR7696207_marked.brca1.bam -
samtools view -h SRR8517856_marked_fixed.bam chr17:43044295-43170245|samtools sort -o SRR7696207_marked_fixed.brca1.bam -

得到的brca1.bam文件如下

ls -lh *brca1.bam
-rwxrwxrwx 1 root root 661K Jun  7 14:26 SRR7696207_bqsr.brca1.bam
-rwxrwxrwx 1 root root 420K Jun  7 14:26 SRR7696207.brca1.bam
-rwxrwxrwx 1 root root 422K Jun  7 14:29 SRR7696207_marked.brca1.bam
-rwxrwxrwx 1 root root 423K Jun  7 14:27 SRR7696207_marked_fixed.brca1.bam

为上述所有brca1.bam文件构建index

ls *.brca1.bam|xargs -i samtools index {}

-rwxrwxrwx 1 root root 661K Jun  7 14:26 SRR7696207_bqsr.brca1.bam
-rwxrwxrwx 1 root root  48K Jun  7 14:31 SRR7696207_bqsr.brca1.bam.bai
-rwxrwxrwx 1 root root 420K Jun  7 14:26 SRR7696207.brca1.bam
-rwxrwxrwx 1 root root  48K Jun  7 14:31 SRR7696207.brca1.bam.bai
-rwxrwxrwx 1 root root 422K Jun  7 14:29 SRR7696207_marked.brca1.bam
-rwxrwxrwx 1 root root  48K Jun  7 14:31 SRR7696207_marked.brca1.bam.bai
-rwxrwxrwx 1 root root 423K Jun  7 14:27 SRR7696207_marked_fixed.brca1.bam
-rwxrwxrwx 1 root root  48K Jun  7 14:31 SRR7696207_marked_fixed.brca1.bam.bai

把上述文件下载到本地IGV查看
注意，igv同时需要.bam和相应的.bai文件，所以需要把整个文件夹cp。