Closed Hello, I try to use bcftools norm with the command : bcftools view --threads 6 \ -f .,PASS \ ${TMP_DIR}/${VCF} \ --regions-file ${interval} \ | \ bcftools norm \ -m - -w 10000 -f ${FASTA} --output-type z --output ${VCF_DIR}/${VCF/vcf.gz/select.vcf.gz} ...
-S, --samples-file[^]FILE:一行一个样本,用法与-s用法相同,只是样本会被写在结尾。bcftools call接受可选的第二列,该列指示倍性(0,1或2)或性别(由--ploidy定义,例如“F”或“M”)。 2. bcftools annotate[OPTIONS]FILE (1)注释VCF文件 bcftools annotate -a db.vcf -c ID,QUAL,+TAG view.vcf -o...
Have a look at section 1.6.2 of the VCF spec (http://samtools.github.io/hts-specs/VCFv4.3.pdf). It describes the genotype ordering of Number=G fields. For the ref (R) and two alt (A,B) alleles you have, the order of the PL fields is RR,RA,AA,RB,AB,BB and the split is ...
挑选IMPACT synonymous_variant及以上的位点,需先经VEP注释,IMPACT 顺序为/bi/database/VEPseverity.txt ,运行插件前需导出环境变量( export BCFTOOLS_PLUGINS=/bi/software/bcftools-1.6/plugins; )也可加入~/.bashrc bcftools +split-vep -S /bi/database/VEPseverity.txt -s all:synonymous_variant+ -x /bi/...
文件tab-delimited##bcftools_normCommand=norm -m-both -o genome_split.vcfgenome.vcf.gz ##bcftools_normCommand=norm -f /home/cmccabe/Desktop/NGS/picard-tools-1.140/resources/a[2] : "DP=num_Miss 浏览0提问于2017-11-30得票数1 回答已采纳 ...
以泰克的示波器MSO54举例说明,标称参数为:2GHZ 6.25GS/s 4ms/div :示波器水平轴上每格的时间宽度为4ms; 40ms :示波器水平轴上总的时间宽度,4ms/div10div=40ms SR:21.25MS/s :表示当前示波器的采样率(sampling rate) 32ns/pt: 在当前的采样率下,采样一个点时间为32ns RL(Record Length):1.25Mp... ...
$ bcftools filter -i ' FILTER=="PASS" && DP>20 && GQ>100 && QUAL>100' "$outDIR"_norm/"$out_basen (3) 提取 突变位点的AD和DP,顺便可以计算 VAF: $ bcftools query-f'[%AD]\n'"$outDIR"/"$out_basename"|awk'BEGIN{FS=","}{ print $2 }'>>"$outDIR"_tmp/"$out_basename"_AD...
Usage: samtools sort [-n] [-m<maxMem>]<in.bam><out.prefix>Options: -m 设置运行内存大小,默认是500,000,000(即500M,支持K/M/G缩写)。对于处理大数据时,如果内存够用,可设置大些,以节约时间。 -n 设定排序方式,按short reads的ID排序。默认下是按序列在fasta文件中的顺序(即header和序列从左往右的...
$ bcftools norm --fasta-ref "$fasta_file" --multiallelics -both --output "$outDIR"_norm/"$out_basename" --output-type z "$inputVCF" image.png (2) 根据条件进行筛选,比如:筛选出FILTER列是PASS的,DP >20 , GQ >100, QUAL >100的位点: ...
norm left-align and normalize indels plugin user-defined plugins query transform VCF/BCF into user-defined formats reheader modify VCF/BCF header, change sample names sort sort VCF/BCF file view VCF/BCF conversion, view, subset and filter VCF/BCF files ...