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WES分析
记录GATK的学习过程
Li_zheng_nan
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WES分析9-过滤&注释
过滤&注释wkd=/home/lzn/WESref=/home/lzn/WES/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fastagatk FilterMutectCalls \-R $ref\-V $wkd/mutect/GSM2653854.vcf \-O $wkd/mutect/GSM2653854.filtered.vcf#A USER ERROR has occurred: Mutect stats t原创 2021-03-29 01:19:55 · 457 阅读 · 0 评论 -
WES分析8-深度&覆盖度
深度&覆盖度wkd=/home/lzn/WESref=/home/lzn/WES/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fastamkdir $wkd/bamqc#qualimapmkdir $wkd/bamqc/qualimapfor sample in `cat $wkd/sample.list`doqualimap bamqc -bam $wkd/align/$sample.sorted.dedup.re原创 2021-03-29 01:19:25 · 516 阅读 · 0 评论 -
WES分析7-VCF
VCF方式一:samtools mpileup 和bcftools call 流程ref=/home/lzn/WES/genome/resources_broad_hg38_v0_Homo_sapiens_assembly38.fastawkd=/home/lzn/WESmkdir $wkd/vcffor sample in `cat $wkd/sample.list`dosamtools mpileup -ugf $ref $wkd/align/$sample.sorted.dedup.原创 2021-03-29 01:18:47 · 710 阅读 · 0 评论 -
WES分析6-BaseRecalibrator
Base Recalibratorsnp=/home/lzn/WES/genome/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf.gzindel=/home/lzn/WES/genome/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gzdbsnp=/home/lzn/WES/genome/resources_broad_原创 2021-03-29 01:17:30 · 1302 阅读 · 0 评论 -
WES分析5-比对
比对cd /home/lzn/WES/genome#参考基因组位于该目录下mkdir index#hisat2 建立indexhisat2-build -p 8 -q hg38.fa.gz ./index/hg38 &#使用软件建立index使用时间较长,还是从hisat2官网下载已经建立好的indexwget https://genome-idx.s3.amazonaws.com/hisat/grch38_snptran.tar.gz#数据存储在Amazon Web Servi原创 2021-03-29 01:16:53 · 550 阅读 · 0 评论 -
WES分析4-质控
质控#/home/lzn/WES/rawdata/mkdir qcfastqc -t 8 -o qc *.fastq &multiqc qc/firefox multiqc_report.html#查看数据质量#测序数据质量比较好直接进行后续分析#之前进行数据质控的代码cat data_id.txt| while read f1 f2; do java -jar ~/trimmomatic/trimmomatic-0.38.jar PE -threads 8 $f1.fastq原创 2021-03-29 01:16:05 · 447 阅读 · 0 评论 -
WES分析3-数据下载
数据下载GSM2653854 HCC1-Tissue GSM2653855 HCC3-TissueGSM2746362 Healthy1-Tissue#数据下载cat SRR_Acc_List.txt |xargs -i prefetch -p {} &# 将每个sample对应的文件放入以sample命名的文件夹中#/home/lzn/WES/rawdata/ls -l ~/wendang/WES/rawdata/|grep GSM*|awk '{print $9}'|xargs原创 2021-03-29 01:15:32 · 475 阅读 · 1 评论 -
WES分析2-分析流程
WES分析流程Data pre-processing for variant discoverymap the sequence reads to the reference genome to produce a file in SAM/BAM format sorted by coordinate.mark duplicates to mitigate biases introduced by data generation steps such as PCR amplification.re原创 2021-03-29 01:14:47 · 1323 阅读 · 0 评论 -
WES分析1-外显子测序
外显子测序外显子(人类基因组的蛋白质编码区)占基因组的不到2%,但含有约85%的已知疾病相关变异体。外显子测序原理针对外显子序列设计捕获探针,与外显子DNA序列相互补。探针上标记有生物素。基因组DNA进行超声打断,与捕获探针杂交。利用探针上生物素与带有链霉亲和素的磁珠结合,通过富集磁珠间接地获得全外显子测序文库。外显子测序中4种无效数据外显子捕获过程中,外显子序列与探针杂交不精确(目标序列有同源序列)。外显子捕获些序列一部分在目标区域,另一部分是紧挨目标区域的邻近序列。dup原创 2021-03-29 01:08:43 · 1779 阅读 · 1 评论