建立失败vcf的索引 成功的vcf会自动构建索引 #失败在第7条染色体,所以这样命名 gatk IndexFeatureFile -F Ran.7.g.vcf 提取前6条正确的vcf, #$genome是基因组文件 gatk SelectVariants -R $genome -V Ran.7.g.vcf -L ran.intervals -O Ran.1_6.g.vcf ran.intervals是数字1到6代表前六条染色体。
samtools faidx human_g1k_v37.fasta > human_g1k_v37.fai 2. 执行以下命令给vcf文件加index。 gatk IndexFeatureFile -F dbsnp132_20101103.vcf gatk BaseRecalibrator -I SRR7_markdup.bam --known-sites dbsnp132_20101103.vcf -O SRR7_bqsr.bam -R human_g1k_v37.fasta gatk ApplyBQSR -bqsr SRR7_...
#下载下来的其实是.gz文件,后续命令可以直接调用gz文件,也可以解压之后再调用,但必须每个都先做index,出来.idx文件,不然做VQSR的时候会报错 $ gatk IndexFeatureFile -I resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf 3. 网站上直接下下来的,虽然后缀是vcf,但有可能实际上是gz文件...
先是进行VariantRecalibrator #VQSR,都要用GATK IndexFeatureFile产生indexhapmap=~/gatk_files/hapmap_3.3.b37.vcfomni=~/gatk_files/1000G_omni2.5.b37.vcfkG=~/gatk_files/1000G_phase1.snps.high_confidence.b37.vcfdbsnp=~/gatk_files/dbsnp_138.b37.vcf#SNP$gatk VariantRecalibrat...
6. 对排序后的vcf文件进行压缩并构建Index bgzip mgp_REL2021_snps.pass.sorted.vcf bgzip mgp_REL2021_indels.pass.sorted.vcf gatk IndexFeatureFile -I mgp_REL2021_snps.pass.sorted.vcf.gz gatk IndexFeatureFile -I mgp_REL2021_indels.pass.sorted.vcf.gz ...
This tab completion functionality has only been tested in the bash shell, and is released as a beta feature. To enable tab completion for the GATK, open a terminal window and source the included tab completion script: source gatk-completion.sh Sourcing this file will allow you to press the...
..found transcripts of type exonBoundary Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'x' in selecting a method for function 'mcols': Unable to find index for BAM file '../5...
bgzip${sampleName}_final.vcfbcftools index${sampleName}_final.vcf.gz 以上就是gatk基于WGS数据检测线粒体SNP/INDEL的最佳分析流程。 04 合并多个样本的vcf文件 涉及到群体基因组分析通常需要合并所有样本vcf文件,这里可以使用bcftools merge 工具实现。
Each line in the sample name map file may now optionally contain a third column with the path/URI to the index. This is useful when the index is not in the same location as the corresponding GVCF. Bug Fixes Fixed an issue where we weren't properly merging AD values when combining GVCFs...
GATK使用说明及流程 1. 要分析的序列名称中,一般不要有空格 2. 准备Reference文件(需为fasta格式)及比 1) Index处理:生成一个ref.fasta.fai 的文件 2) 生成.dict文件: samtoolsfaidxreference.fasta java -jarpicard-tools/CreateSequenceDictionary.jar R=reference.fasta O=reference.dict bwaindex-abwtswref....