8 GATK完整流程

总目录:三阴性乳腺癌全外显子分析(wes)

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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

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GATK的参考

GATK Pipeline for calling variants from one sample
Variant Calling Pipeline: FastQ to Annotated SNPs in Hours

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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