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。这里就看它对应的idx文件是否为".gz.idx"文件了,如果是,你就重新命名一下,把原始文件改成“vcf.gz”就好了 生成vcf文件 单样本到这一步就可以生成VCF了 使用HaplotypeCaller对上述的bam文件进行call variant,就是寻找变异的过程,生成一个VCF文件...
gatk MergeVcfs -I seg1_1.vcf -I seg1_2.vcf -I seg1_3.vcf -O xxx.vcf ## 合并命令 合并结果如下: [root@PC1 test]# ls seg1_1.vcf seg1_2.vcf seg1_3.vcf xxx.vcf xxx.vcf.idx [root@PC1 test]#ll-htotal2.4G-rw-r--r--.1root root 392M Dec118:14seg1_1.vcf-rw-r--...
g1k_idx=config["GATK"]["dir"]+"/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi", dbsnp=config["GATK"]["dir"]+"/Homo_sapiens_assembly38.dbsnp138.vcf.gz", dbsnp_idx=config["GATK"]["dir"]+"/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi", hapmap=config["GATK"]["dir"]+"/ha...
java -Xmx45g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R IRGSP_v4.fasta -I EV_dedup_realign.bam -glm BOTH -stand_call_conf 30 -stand_emit_conf 10 -o LD.vcf 用GATK工具包 中的UnifiedGenotyper对上述重新比对过的bam文件进行变异检测,寻找variant,此步骤结束会产生一个vcf文件和一个idx文件...
pipeline/GATK/bundle/2.5/hg19/hapmap_3.3.hg19.vcf.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system. ### ERROR --- 这个错误说实话我也不是很清楚,可能是不能同时调用bundle...
pop.raw.vcf.gz 注：gatk4.0以后GenotypeGVCFs只能接受single-sample GVCF ，若有多个g.vcf 可以...
这个错误说明你的输入文件(原始VCF文件)构建的索引文件(.idx)所用的参考基因组,和,你现在所用的knows选项所指定的文件中的索引文件构建所用的参考序列不一致。 ### ERROR --- ### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a): ### ERROR ### ERROR This means that one or more argu...
### ERROR MESSAGE: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file raw.vcf.tmp.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system. ###...
"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx", "PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [ "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz", ...
hapmap_3.3.hg19.vcf.idx Mills_and_1000G_gold_standard.indels.hg19.vcf Mills_and_1000G_gold_standard.indels.hg19.vcf.idx (3)R 设置 GATK某些步骤需要使用R画一些图,此时会调用一些R packages。如果你使用的R没有装这些packages,就无法生成pdf文件。因此得安装一些必要的R packages,包括(但不限于)如下:...