总目录:三阴性乳腺癌全外显子分析(wes)
建议读或观看以下内容
1 深入了解snp-calling流程
2 Cloud Computing for Next-Generation Sequencing Data Analysis
3 https://en.wikipedia.org/wiki/SNV_calling_from_NGS_data
4Small-Variant Calling and Annotation
5 Hands-on Tutorial on SNP Calling
6 Finding SNPs Using Sequencing Data
GATK的参考
GATK Pipeline for calling variants from one sample
Variant Calling Pipeline: FastQ to Annotated SNPs in Hours
1 sort 和index
sort the reads by coordinate, save as a bam file and index the bam file
上一部分已经以 coordinate sort处理完毕。接下来进行index
cat /project/align/wes/bamfile10|while read id;
do
samtools index $id
done
或直接
samtools index *.bam
